Hi all,

When I do GetPileupSummaries for the following CalculateContamination analysis, an error arose about input vcf.

a) GATK version used: gatk-4.1.9.0

b) Exact command used:

 gatk GetPileupSummaries \
-I normal_sorted_align_mD_rc_rRG.bam \
-V gnomad.exomes.r2.1.1.sites_withchr.vcf.gz \
-L exome_calling_regions.v1_withchr.interval_list \
-O normal_pileups.table

c) Entire error log:

14:52:11.558 INFO  ProgressMeter -       chr11:47376795             70.9               4606000          64962.1
14:52:21.958 INFO  ProgressMeter -       chr11:55541279             71.1               4615000          64930.3
14:52:27.874 INFO  GetPileupSummaries - Shutting down engine
[August 16, 2021 at 2:52:27 PM JST] org.broadinstitute.hellbender.tools.walkers.contamination.GetPileupSummaries done. Elapsed time: 71.21 minutes.
Runtime.totalMemory()=3175088128
htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 2746209: The VCF specification does not allow for whitespace in the INFO field. Offending field value was "AC=12;AN=205402;AF=5.8422e-05;rf_tp_probability=0.852059;FS=3.525;InbreedingCoeff=0.0081;MQ=60;MQRankSum=-0.374;QD=12.02;ReadPosRankSum=0.295;SOR=0.966;BaseQRankSum=-1.543;ClippingRankSum=0;DP=3874916;VQSLOD=1.89;VQSR_culprit=FS;variant_type=mixed;allele_type=snv;n_alt_alleles=2;was_mixed;pab_max=1;gq_hist_alt_bin_freq=0|0|0|0|0|1|0|1|0|0|0|0|0|0|0|0|0|1|0|10;gq_hist_all_bin_freq=1516|3475|2738|7439|9794|5567|10834|10090|4670|8223|7065|3107|7966|1698|3423|1916|3687|873|3345|27823;dp_hist_alt_bin_freq=0|0|6|1|2|2|1|0|0|1|0|0|0|0|0|0|0|0|0|0;dp_hist_alt_n_larger=0;dp_hist_all_bin_freq=5228|16377|24510|21469|15506|8368|8570|15436|7175|1725|551|283|161|101|101|71|36|35|15|21;dp_hist_all_n_larger=9;ab_hist_alt_bin_freq=0|0|0|1|0|0|0|0|1|1|1|2|4|1|1|0|1|0|0|0;AC_nfe_seu=0;AN_nfe_seu=7514;AF_nfe_seu=0;nhomalt_nfe_seu=0;controls_AC_afr_male=0;controls_AN_afr_male=2136;controls_AF_afr_male=0;controls_nhomalt_afr_male=0;non_neuro_AC_eas_kor=0;non_neuro_AN_eas_kor=3516;non_neuro_AF_eas_kor=0;non_neuro_nhomalt_eas_kor=0;non_topmed_AC_amr=12;non_topmed_AN_amr=30026;non_topmed_AF_amr=0.000399654;non_topmed_nhomalt_amr=0;non_cancer_AC_asj_female=0;non_cancer_AN_asj_female=3986;non_cancer_AF_asj_female=0;non_cancer_nhomalt_asj_female=0;AC_raw=13;AN_raw=250498;AF_raw=5.18966e-05;nhomalt_raw=0;AC_fin_female=0;AN_fin_female=8890;AF_fin_female=0;nhomalt_fin_female=0;non_cancer_AC_oth_female=0;non_cancer_AN_oth_female=2280;non_cancer_AF_oth_female=0;non_cancer_nhomalt_oth_female=0;AC_nfe_bgr=0;AN_nfe_bgr=1732;AF_nfe_bgr=0;nhomalt_nfe_bgr=0;non_neuro_AC_asj_female=0;non_neuro_AN_asj_female=2420;non_neuro_AF_asj_female=0;non_neuro_nhomalt_asj_female=0;AC_sas_male=0;AN_sas_male=20286;AF_sas_male=0;nhomalt_sas_male=0;non_neuro_AC_afr_male=0;non_neuro_AN_afr_male=4670;non_neuro_AF_afr_male=0;non_neuro_nhomalt_afr_male=0;AC_afr_male=0;AN_afr_male=4688;AF_afr_male=0;nhomalt_afr_male=0;AC_afr=0;AN_afr=11300;AF_afr=0;nhomalt_afr=0;controls_AC_nfe_swe=0;controls_AN_nfe_swe=9574;controls_AF_nfe_swe=0;controls_nhomalt_nfe_swe=0;non_neuro_AC_afr_female=0;non_neuro_AN_afr_female=6598;non_neuro_AF_afr_female=0;non_neuro_nhomalt_afr_female=0;non_topmed_AC_amr_female=9;non_topmed_AN_amr_female=17426;non_topmed_AF_amr_female=0.00051647;non_topmed_nhomalt_amr_female=0;non_cancer_AC_female=9;non_cancer_AN_female=88070;non_cancer_AF_female=0.000102191;non_cancer_nhomalt_female=0;non_cachr16      2549972 rs370235069     T       A       50080.7      PASS    AC=26;AN=248606;AF=0.000104583;rf_tp_probability=0.918423;FS=0;InbreedingCoeff=0.0028;MQ=59.4;MQRankSum=0.22;QD=13.85;ReadPosRankSum=0.531;SOR=0.665;BaseQRankSum=1.37;ClippingRankSum=0.117;DP=14668394;VQSLOD=5.58;VQSR_culprit=FS;variant_type=snv;allele_type=snv;n_alt_alleles=1;has_star;pab_max=1;gq_hist_alt_bin_freq=0|0|0|0|0|0|0|0|0|0|0|0|1|0|0|0|0|0|0|26;gq_hist_all_bin_freq=322|211|53|197|301|184|480|555|360|793|1156|857|3381|1093|3036|1750|4842|1007|5154|99532;dp_hist_alt_bin_freq=0|1|0|0|0|1|0|0|2|1|2|2|0|0|2|3|2|0|3|0;dp_hist_alt_n_larger=8;dp_hist_all_bin_freq=1005|397|807|956|2369|4602|6684|10176|14000|10425|6863|5880|5394|5035|4383|3926|3512|2964|2510|2416;dp_hist_all_n_larger=31444;ab_hist_alt_bin_freq=0|0|0|0|0|0|1|1|5|11|5|2|1|1|0|0|0|0|0|0;AC_nfe_seu=0;AN_nfe_seu=11376;AF_nfe_seu=0;nhomalt_nfe_seu=0;controls_AC_afr_male=0;controls_AN_afr_male=2916;controls_AF_afr_male=0;controls_nhomalt_afr_male=0;non_neuro_AC_eas_kor=0;non_neuro_AN_eas_kor=3814;non_neuro_AF_eas_kor=0;non_neuro_nhomalt_eas_kor=0;non_topmed_AC_amr=0;non_topmed_AN_amr=34344;non_topmed_AF_amr=0;non_topmed_nhomalt_amr=0;non_cancer_AC_asj_female=0;non_cancer_AN_asj_female=4582;non_cancer_AF_asj_female=0;non_cancer_nhomalt_asj_female=0;AC_raw=27;AN_raw=250528;AF_raw=0.000107772;nhomalt_raw=0;AC_fin_female=0;AN_fin_female=10314;AF_fin_female=0;nhomalt_fin_female=0;non_cancer_AC_oth_female=0;non_cancer_AN_oth_female=2626;non_cancer_AF_oth_female=0;non_cancer_nhomalt_oth_female=0;AC_nfe_bgr=0;AN_nfe_bgr=2664;AF_nfe_bgr=0;nhomalt_nfe_bgr=0;non_neuro_AC_asj_female=0;non_neuro_AN_asj_female=3062;non_neuro_AF_asj_female=0;non_neuro_nhomalt_asj_female=0;AC_sas_male=0;AN_sas_male=23066;AF_sas_male=0;nhomalt_sas_male=0;non_neuro_AC_afr_male=0;non_neuro_AN_afr_male=6146;non_neuro_AF_afr_male=0;non_neuro_nhomalt_afr_male=0;AC_afr_male=0;AN_afr_male=6166;AF_afr_male=0;nhomalt_afr_male=0;AC_afr=0;AN_afr=15456;AF_afr=0;nhomalt_afr=0;controls_AC_nfe_swe=1;controls_AN_nfe_swe=12802;controls_AF_nfe_swe=7.81128e-05;controls_nhomalt_nfe_swe=0;non_neuro_AC_afr_female=0;non_neuro_AN_afr_female=9274;non_neuro_AF_afr_female=0;non_neuro_nhomalt_afr_female=0;non_topmed_AC_amr_female=0;non_topmed_AN_amr_female=20132;non_topmed_AF_amr_female=0;non_topmed_nhomalt_amr_female=0;non_cancer_AC_female=11;non_cancer_AN_female=105896;non_cancer_AF_female=0.000103876;non_cancer_nhomalt_female=0;non_cancer_AC_nfe_onf=10;non_cancer_AN_nfe_onf=24392;non_cancer_AF_nfe_onf=0.00040997;non_cancer_nhomalt_nfe_onf=0;non_cancer_AC_male=13;non_cancer_AN_male=128420;non_cancer_AF_male=0.00010123;non_cancer_nhomalt_male=0;non_topmed_AC_oth_female=0;non_topmed_AN_oth_female=2824;non_topmed_AF_oth_female=0;non_topmed_nhomalt_oth_female=0;AC_eas_female=0;AN_eas_female=9126;AF_eas_female=0;nhomalt_eas_female=0;non_cancer_AC_sas_female=0;non_cancer_AN_sas_female=7484;non_cancer_AF_sas_female=0;non_cancer_nhomalt_sas_female=0;AC_afr_female=0;AN_afr_female=9290;AF_afr_female=0;nhomalt_afr_female=0;AC_sas=0;AN_sas=30598;AF_sas=0;nhomalt_sas=0;non_neuro_AC_female=10;non_neuro_AN_female=93720;non_neuro_AF_female=0.000106701;non_neuro_nhomalt_female=0;controls_AC_afr=0;controls_AN_afr=7130;controls_AF_afr=0;controls_nhomalt_afr=0;non_neuro_AC_eas_jpn=0;non_neuro_AN_eas_jpn=132;non_neuro_AF_eas_jpn=0;non_neuro_nhomalt_eas_jpn=0;AC_nfe_onf=10;AN_nfe_onf=30614;AF_nfe_onf=0.000326648;nhomalt_nfe_onf=0;non_cancer_AC_amr_male=0;non_cancer_AN_amr_male=14122;non_cancer_AF_amr_male=0;non_cancer_nhomalt_amr_male=0;controls_AC_fin_male=0;controls_AN_fin_male=6890;controls_AF_fin_male=0;controls_nhomalt_fin_male=0;non_neuro_AC_nfe_nwe=13;non_neuro_AN_nfe_nwe=34656;non_neuro_AF_nfe_nwe=0.000375115;non_neuro_nhomalt_nfe_nwe=0;AC_fin_male=0;AN_fin_male=11240;AF_fin_male=0;nhomalt_fin_male=0;AC_nfe_female=12;AN_nfe_female=49346;AF_nfe_female=0.000243181;nhomalt_nfe_female=0;AC_amr=0;AN_amr=34478;AF_amr=0;nhomalt_amr=0;non_topmed_AC_nfe_male=14;non_topmed_AN_nfe_male=62364;non_topmed_AF_nfe_male=0.000224488;non_topmed_nhomalt_nfe_male=0;non_neuro_AC_sas=0;non_neuro_AN_sas=30590;non_neuro_AF_sas=0;non_neuro_nhomalt_sas=0;non_cancer_AC_fin_male=0;non_cancer_AN_fin_male=11236;non_cancer_AF_fin_male=0;non_cancer_nhomalt_fin_male=0;non_cancer_AC_nfe_seu=0;non_cancer_AN_nfe_seu=10496;non_cancer_AF_nfe_seu=0;non_cancer_nhomalt_nfe_seu=0;AC_eas=0;AN_eas=17972;AF_eas=0;nhomalt_eas=0;nhomalt=0;non_neuro_AC_nfe_female=10;non_neuro_AN_nfe_female=39082;non_neuro_AF_nfe_female=0.000255872;non_neuro_nhomalt_nfe_female=0;non_neuro_AC_afr=0;non_neuro_AN_afr=15420;non_neuro_AF_afr=0;non_neuro_nhomalt_afr=0;controls_AC_raw=8;controls_AN_raw=108900;controls_AF_raw=7.34619e-05;controls_nhomalt_raw=0;non_cancer_AC_eas=0;non_cancer_AN_eas=17282;non_cancer_AF_eas=0;non_cancer_nhomalt_eas=0;non_cancer_AC_amr_female=0;non_cancer_AN_amr_female=20028;non_cancer_AF_amr_female=0;non_cancer_nhomalt_amr_female=0;non_neuro_AC_nfe_swe=2;non_neuro_AN_nfe_swe=14724;non_neuro_AF_nfe_swe=0.000135833;non_neuro_nhomalt_nfe_swe=0;controls_AC_male=4;controls_AN_male=57726;controls_AF_male=6.92929e-05;controls_nhomalt_male=0;non_topmed_AC_male=14;non_topmed_AN_male=132686;non_topmed_AF_male=0.000105512;non_topmed_nhomalt_male=0;controls_AC_eas_jpn=0;controls_AN_eas_jpn=96;controls_AF_eas_jpn=0;controls_nhomalt_eas_jpn=0;controls_AC_nfe_female=4;controls_AN_nfe_female=19048;controls_AF_nfe_female=0.000209996;controls_nhomalt_nfe_female=0;non_neuro_AC_amr=0;non_neuro_AN_amr=30418;non_neuro_AF_amr=0;non_neuro_nhomalt_amr=0;non_neuro_AC_eas_female=0;non_neuro_AN_eas_female=6642;non_neuro_AF_eas_female=0;non_neuro_nhomalt_eas_female=0;AC_asj_male=0;AN_asj_male=5174;AF_asj_male=0;nhomalt_asj_male=0;controls_AC_nfe_male=4;controls_AN_nfe_male=23542;controls_AF_nfe_male=0.000169909;controls_nhomalt_nfe_male=0;non_neuro_AC_fin=0;non_neuro_AN_fin=16646;non_neuro_AF_fin=0;non_neuro_nhomalt_fin=0;non_topmed_AC_sas=0;non_topmed_AN_sas=30598;non_topmed_AF_sas=0;non_topmed_nhomalt_sas=0;non_cancer_AC_nfe_female=11;non_cancer_AN_nfe_female=43658;non_cancer_AF_nfe_female=0.000251958;non_cancer_nhomalt_nfe_female=0;AC_oth_female=0;AN_oth_female=2866;AF_oth_female=0;nhomalt_oth_female=0;non_cancer_AC_asj=0;non_cancer_AN_asj=9554;non_cancer_AF_asj=0;non_cancer_nhomalt_asj=0;AC_nfe_swe=3;AN_nfe_swe=26064;AF_nfe_swe=0.000115101;nhomalt_nfe_swe=0;controls_AC_nfe=8;controls_AN_nfe=42590;controls_AF_nfe=0.000187838;controls_nhomalt_nfe=0;controls_AC_oth_female=0;controls_AN_oth_female=978;controls_AF_oth_female=0;controls_nhomalt_oth_female=0;controls_AC_asj=0;controls_AN_asj=2320;controls_AF_asj=0;controls_nhomalt_asj=0;non_neuro_AC_amr_male=0;non_neuro_AN_amr_male=12210;non_neuro_AF_amr_male=0;non_neuro_nhomalt_amr_male=0;controls_AC_nfe_nwe=5;controls_AN_nfe_nwe=14382;controls_AF_nfe_nwe=0.000347657;controls_nhomalt_nfe_nwe=0;AC_nfe_nwe=13;AN_nfe_nwe=41494;AF_nfe_nwe=0.000313298;nhomalt_nfe_nwe=0;controls_AC_nfe_seu=0;controls_AN_nfe_seu=4694;controls_AF_nfe_seu=0;controls_nhomalt_nfe_seu=0;controls_AC_sas_female=0;controls_AN_sas_female=4206;controls_AF_sas_female=0;controls_nhomalt_sas_female=0;non_neuro_AC_amr_female=0;non_neuro_AN_amr_female=18208;non_neuro_AF_amr_female=0;non_neuro_nhomalt_amr_female=0;non_cancer_AC_eas_jpn=0;non_cancer_AN_eas_jpn=106;non_cancer_AF_eas_jpn=0;non_cancer_nhomalt_eas_jpn=0;non_neuro_AC_nfe_onf=7;non_neuro_AN_nfe_onf=27486;non_neuro_AF_nfe_onf=0.000254675;non_neuro_nhomalt_nfe_onf=0;non_topmed_AC_eas_male=0;non_topmed_AN_eas_male=8842;non_topmed_AF_eas_male=0;non_topmed_nhomalt_eas_male=0;AC_eas_jpn=0;AN_eas_jpn=134;AF_eas_jpn=0;nhomalt_eas_jpn=0;non_cancer_AC_afr_male=0;non_cancer_AN_afr_male=5652;non_cancer_AF_afr_male=0;non_cancer_nhomalt_afr_male=0;non_cancer_AC_afr=0;non_cancer_AN_afr=14110;non_cancer_AF_afr=0;non_cancer_nhomalt_afr=0;controls_AC_amr_female=0;controls_AN_amr_female=10188;controls_AF_amr_female=0;controls_nhomalt_amr_female=0;non_neuro_AC_fin_male=0;non_neuro_AN_fin_male=9054;non_neuro_AF_fin_male=0;non_neuro_nhomalt_fin_male=0;AC_female=12;AN_female=113556;AF_female=0.000105675;nhomalt_female=0;non_neuro_AC_nfe_bgr=0;non_neuro_AN_nfe_bgr=448;non_neuro_AF_nfe_bgr=0;non_neuro_nhomalt_nfe_bgr=0;non_neuro_AC_oth_male=0;non_neuro_AN_oth_male=2450;non_neuro_AF_oth_male=0;non_neuro_nhomalt_oth_male=0;non_topmed_AC_nfe_est=0;non_topmed_AN_nfe_est=236;non_topmed_AF_nfe_est=0;non_topmed_nhomalt_nfe_est=0;non_topmed_AC_nfe_nwe=12;non_topmed_AN_nfe_nwe=40374;non_topmed_AF_nfe_nwe=0.000297221;non_topmed_nhomalt_nfe_nwe=0;non_topmed_AC_amr_male=0;non_topmed_AN_amr_male=14212;non_topmed_AF_amr_male=0;non_topmed_nhomalt_amr_male=0;non_cancer_AC_amr=0;non_cancer_AN_amr=34150;non_cancer_AF_amr=0;non_cancer_nhomalt_amr=0;non_topmed_AC_nfe_swe=3;non_topmed_AN_nfe_swe=26002;non_topmed_AF_nfe_swe=0.000115376;non_topmed_nhomalt_nfe_swe=0;non_topmed_AC_nfe_onf=10;non_topmed_AN_nfe_onf=29818;non_topmed_AF_nfe_onf=0.000335368;non_topmed_nhomalt_nfe_onf=0;controls_AC_eas_kor=0;controls_AN_eas_kor=1888;controls_AF_eas_kor=0;controls_nhomalt_eas_kor=0;non_topmed_AC_eas_oea=0;non_topmed_AN_eas_oea=14018;non_topmed_AF_eas_oea=0;non_topmed_nhomalt_eas_oea=0;controls_AC_eas_male=0;controls_AN_eas_male=4038;controls_AF_eas_male=0;controls_nhomalt_eas_male=0;controls_AC_oth_male=0;controls_AN_oth_male=918;controls_AF_oth_male=0;controls_nhomalt_oth_male=0;non_topmed_AC=25;non_topmed_AN=242100;non_topmed_AF=0.000103263;non_topmed_nhomalt=0;controls_AC_fin=0;controls_AN_fin=13306;controls_AF_fin=0;controls_nhomalt_fin=0;AC_eas_kor=0;AN_eas_kor=3816;AF_eas_kor=0;nhomalt_eas_kor=0;non_neuro_AC_nfe=22;non_neuro_AN_nfe=88366;non_neuro_AF_nfe=0.000248965;non_neuro_nhomalt_nfe=0;non_neuro_AC_fin_female=0;non_neuro_AN_fin_female=7592;non_neuro_AF_fin_female=0;non_neuro_nhomalt_fin_female=0;non_cancer_AC_nfe_male=13;non_cancer_AN_nfe_male=57978;non_cancer_AF_nfe_male=0.000224223;non_cancer_nhomalt_nfe_male=0;controls_AC_eas_oea=0;controls_AN_eas_oea=6652;controls_AF_eas_oea=0;controls_nhomalt_eas_oea=0;non_topmed_AC_nfe_seu=0;non_topmed_AN_nfe_seu=11280;non_topmed_AF_nfe_seu=0;non_topmed_nhomalt_nfe_seu=0;controls_AC_eas_female=0;controls_AN_eas_female=4598;controls_AF_eas_female=0;controls_nhomalt_eas_female=0;non_topmed_AC_asj=0;non_topmed_AN_asj=9966;non_topmed_AF_asj=0;non_topmed_nhomalt_asj=0;controls_AC_nfe_onf=2;controls_AN_nfe_onf=9964;controls_AF_nfe_onf=0.000200723;controls_nhomalt_nfe_onf=0;non_neuro_AC=22;non_neuro_AN=205402;non_neuro_AF=0.000107107;non_neuro_nhomalt=0;AC_eas_oea=0;AN_eas_oea=14022;AF_eas_oea=0;nhomalt_eas_oea=0;non_topmed_AC_nfe=25;non_topmed_AN_nfe=110366;non_topmed_AF_nfe=0.000226519;non_topmed_nhomalt_nfe=0;non_cancer_AC_oth=0;non_cancer_AN_oth=5536;non_cancer_AF_oth=0;non_cancer_nhomalt_oth=0;non_topmed_AC_raw=26;non_topmed_AN_raw=243940;non_topmed_AF_raw=0.000106584;non_topmed_nhomalt_raw=0;non_neuro_AC_nfe_est=0;non_neuro_AN_nfe_est=214;non_neuro_AF_nfe_est=0;non_neuro_nhomalt_nfe_est=0;non_topmed_AC_oth_male=0;non_topmed_AN_oth_male=3158;non_topmed_AF_oth_male=0;non_topmed_nhomalt_oth_male=0;non_cancer_AC_oth_male=0;non_cancer_AN_oth_male=2910;non_cancer_AF_oth_male=0;non_cancer_nhomalt_oth_male=0;AC_nfe_est=0;AN_nfe_est=240;AF_nfe_est=0;nhomalt_nfe_est=0;non_cancer_AC_afr_female=0;non_cancer_AN_afr_female=8458;non_cancer_AF_afr_female=0;non_cancer_nhomalt_afr_female=0;non_topmed_AC_afr_male=0;non_topmed_AN_afr_male=4666;non_topmed_AF_afr_male=0;non_topmed_nhomalt_afr_male=0;AC_eas_male=0;AN_eas_male=8846;AF_eas_male=0;nhomalt_eas_male=0;controls_AC_eas=0;controls_AN_eas=8636;controls_AF_eas=0;controls_nhomalt_eas=0;non_neuro_AC_eas_male=0;non_neuro_AN_eas_male=6354;non_neuro_AF_eas_male=0;non_neuro_nhomalt_eas_male=0;non_cancer_AC_nfe_nwe=12;non_cancer_AN_nfe_nwe=38826;non_cancer_AF_nfe_nwe=0.000309071;non_cancer_nhomalt_nfe_nwe=0;controls_AC_sas=0;controls_AN_sas=15676;controls_AF_sas=0;controls_nhomalt_sas=0;non_neuro_AC_sas_male=0;non_neuro_AN_sas_male=23060;non_neuro_AF_sas_male=0;non_neuro_nhomalt_sas_male=0;non_neuro_AC_asj_male=0;non_neuro_AN_asj_male=3124;non_neuro_AF_asj_male=0;non_neuro_nhomalt_asj_male=0;non_cancer_AC_nfe_bgr=0;non_cancer_AN_nfe_bgr=2520;non_cancer_AF_nfe_bgr=0;non_cancer_nhomalt_nfe_bgr=0;controls_AC_oth=0;controls_AN_oth=1896;controls_AF_oth=0;controls_nhomalt_oth=0;non_cancer_AC_eas_female=0;non_cancer_AN_eas_female=8758;non_cancer_AF_eas_female=0;non_cancer_nhomalt_eas_female=0;AC_nfe=26;AN_nfe=112452;AF_nfe=0.00023121;nhomalt_nfe=0;non_topmed_AC_female=11;non_topmed_AN_female=109414;non_topmed_AF_female=0.000100536;non_topmed_nhomalt_female=0;non_neuro_AC_asj=0;non_neuro_AN_asj=6186;non_neuro_AF_asj=0;non_neuro_nhomalt_asj=0;non_topmed_AC_eas_female=0;non_topmed_AN_eas_female=9126;non_topmed_AF_eas_female=0;non_topmed_nhomalt_eas_female=0;non_neuro_AC_raw=23;non_neuro_AN_raw=207188;non_neuro_AF_raw=0.00011101;non_neuro_nhomalt_raw=0;non_topmed_AC_eas=0;non_topmed_AN_eas=17968;non_topmed_AF_eas=0;non_topmed_nhomalt_eas=0;non_topmed_AC_fin_male=0;non_topmed_AN_fin_male=11240;non_topmed_AF_fin_male=0;non_topmed_nhomalt_fin_male=0;non_cancer_AC_asj_male=0;non_cancer_AN_asj_male=4972;non_cancer_AF_asj_male=0;non_cancer_nhomalt_asj_male=0;AC_fin=0;AN_fin=21554;AF_fin=0;nhomalt_fin=0;AC_nfe_male=14;AN_nfe_male=63106;AF_nfe_male=0.000221849;nhomalt_nfe_male=0;non_topmed_AC_eas_kor=0;non_topmed_AN_eas_kor=3816;non_topmed_AF_eas_kor=0;non_topmed_nhomalt_eas_kor=0;controls_AC_amr_male=0;controls_AN_amr_male=6846;controls_AF_amr_male=0;controls_nhomalt_amr_male=0;non_neuro_AC_eas_oea=0;non_neuro_AN_eas_oea=9050;non_neuro_AF_eas_oea=0;non_neuro_nhomalt_eas_oea=0;AC_sas_female=0;AN_sas_female=7532;AF_sas_female=0;nhomalt_sas_female=0;controls_AC_afr_female=0;controls_AN_afr_female=4214;controls_AF_afr_female=0;controls_nhomalt_afr_female=0;controls_AC_amr=0;controls_AN_amr=17034;controls_AF_amr=0;controls_nhomalt_amr=0;non_topmed_AC_eas_jpn=0;non_topmed_AN_eas_jpn=134;non_topmed_AF_eas_jpn=0;non_topmed_nhomalt_eas_jpn=0;AC_asj_female=0;AN_asj_female=4874;AF_asj_female=0;nhomalt_asj_female=0;non_topmed_AC_nfe_bgr=0;non_topmed_AN_nfe_bgr=2656;non_topmed_AF_nfe_bgr=0;non_topmed_nhomalt_nfe_bgr=0;non_cancer_AC_nfe_est=0;non_cancer_AN_nfe_est=158;non_cancer_AF_nfe_est=0;non_cancer_nhomalt_nfe_est=0;non_neuro_AC_eas=0;non_neuro_AN_eas=12996;non_neuro_AF_eas=0;non_neuro_nhomalt_eas=0;non_cancer_AC_nfe=24;non_cancer_AN_nfe=101636;non_cancer_AF_nfe=0.000236137;non_cancer_nhomalt_nfe=0;non_neuro_AC_male=12;non_neuro_AN_male=111682;non_neuro_AF_male=0.000107448;non_neuro_nhomalt_male=0;non_neuro_AC_sas_female=0;non_neuro_AN_sas_female=7530;non_neuro_AF_sas_female=0;non_neuro_nhomalt_sas_female=0;AC_asj=0;AN_asj=10048;AF_asj=0;nhomalt_asj=0;controls_AC_nfe_est=0;controls_AN_nfe_est=70;controls_AF_nfe_est=0;controls_nhomalt_nfe_est=0;non_topmed_AC_asj_female=0;non_topmed_AN_asj_female=4828;non_topmed_AF_asj_female=0;non_topmed_nhomalt_asj_female=0;non_cancer_AC_nfe_swe=2;non_cancer_AN_nfe_swe=25244;non_cancer_AF_nfe_swe=7.92267e-05;non_cancer_nhomalt_nfe_swe=0;non_cancer_AC=24;non_cancer_AN=234316;non_cancer_AF=0.000102426;non_cancer_nhomalt=0;non_topmed_AC_oth=0;non_topmed_AN_oth=5982;non_topmed_AF_oth=0;non_topmed_nhomalt_oth=0;non_topmed_AC_fin_female=0;non_topmed_AN_fin_female=10312;non_topmed_AF_fin_female=0;non_topmed_nhomalt_fin_female=0;non_cancer_AC_fin_female=0;non_cancer_AN_fin_female=10302;non_cancer_AF_fin_female=0;non_cancer_nhomalt_fin_female=0;AC_oth=0;AN_oth=6048;AF_oth=0;nhomalt_oth=0;non_neuro_AC_nfe_male=12;non_neuro_AN_nfe_male=49284;non_neuro_AF_nfe_male=0.000243487;non_neuro_nhomalt_nfe_male=0;controls_AC_female=4;controls_AN_female=50862;controls_AF_female=7.86442e-05;controls_nhomalt_female=0;non_cancer_AC_fin=0;non_cancer_AN_fin=21538;non_cancer_AF_fin=0;non_cancer_nhomalt_fin=0;non_topmed_AC_fin=0;non_topmed_AN_fin=21552;non_topmed_AF_fin=0;non_topmed_nhomalt_fin=0;non_cancer_AC_eas_oea=0;non_cancer_AN_eas_oea=13402;non_cancer_AF_eas_oea=0;non_cancer_nhomalt_eas_oea=0;non_topmed_AC_nfe_female=11;non_topmed_AN_nfe_female=48002;non_topmed_AF_nfe_female=0.000229157;non_topmed_nhomalt_nfe_female=0;non_cancer_AC_sas_male=0;non_cancer_AN_sas_male=23026;non_cancer_AF_sas_male=0;non_cancer_nhomalt_sas_male=0;controls_AC_asj_male=0;controls_AN_asj_male=1106;controls_AF_asj_male=0;controls_nhomalt_asj_male=0;non_cancer_AC_raw=24;non_cancer_AN_raw=235998;non_cancer_AF_raw=0.000101696;non_cancer_nhomalt_raw=0;non_cancer_AC_eas_male=0;non_cancer_AN_eas_male=8524;non_cancer_AF_eas_male=0;non_cancer_nhomalt_eas_male=0;non_topmed_AC_asj_male=0;non_topmed_AN_asj_male=5138;non_topmed_AF_asj_male=0;non_topmed_nhomalt_asj_male=0;non_neuro_AC_oth=0;non_neuro_AN_oth=4780;non_neuro_AF_oth=0;non_neuro_nhomalt_oth=0;AC_male=14;AN_male=135050;AF_male=0.000103665;nhomalt_male=0;controls_AC_fin_female=0;controls_AN_fin_female=6416;controls_AF_fin_female=0;controls_nhomalt_fin_female=0;controls_AC_nfe_bgr=0;controls_AN_nfe_bgr=678;controls_AF_nfe_bgr=0;controls_nhomalt_nfe_bgr=0;controls_AC_asj_female=0;controls_AN_asj_female=1214;controls_AF_asj_female=0;controls_nhomalt_asj_female=0;AC_amr_male=0;AN_amr_male=14270;AF_amr_male=0;nhomalt_amr_male=0;AC_amr_female=0;AN_amr_female=20208;AF_amr_female=0;nhomalt_amr_female=0;non_topmed_AC_sas_male=0;non_topmed_AN_sas_male=23066;non_topmed_AF_sas_male=0;non_topmed_nhomalt_sas_male=0;AC_oth_male=0;AN_oth_male=3182;AF_oth_male=0;nhomalt_oth_male=0;non_cancer_AC_sas=0;non_cancer_AN_sas=30510;non_cancer_AF_sas=0;non_cancer_nhomalt_sas=0;non_neuro_AC_nfe_seu=0;non_neuro_AN_nfe_seu=10838;non_neuro_AF_nfe_seu=0;non_neuro_nhomalt_nfe_seu=0;non_cancer_AC_eas_kor=0;non_cancer_AN_eas_kor=3774;non_cancer_AF_eas_kor=0;non_cancer_nhomalt_eas_kor=0;non_topmed_AC_afr_female=0;non_topmed_AN_afr_female=6658;non_topmed_AF_afr_female=0;non_topmed_nhomalt_afr_female=0;controls_AC_sas_male=0;controls_AN_sas_male=11470;controls_AF_sas_male=0;controls_nhomalt_sas_male=0;non_topmed_AC_sas_female=0;non_topmed_AN_sas_female=7532;non_topmed_AF_sas_female=0;non_topmed_nhomalt_sas_female=0;non_topmed_AC_afr=0;non_topmed_AN_afr=11324;non_topmed_AF_afr=0;non_topmed_nhomalt_afr=0;controls_AC=8;controls_AN=108588;controls_AF=7.3673e-05;controls_nhomalt=0;non_neuro_AC_oth_female=0;non_neuro_AN_oth_female=2330;non_neuro_AF_oth_female=0;non_neuro_nhomalt_oth_female=0;non_topmed_faf95_amr=0;non_topmed_faf99_amr=0;faf95_afr=0;faf99_afr=0;faf95_sas=0;faf99_sas=0;controls_faf95_afr=0;controls_faf99_afr=0;faf95_amr=0;faf99_amr=0;non_neuro_faf95_sas=0;non_neuro_faf99_sas=0;faf95_eas=0;faf99_eas=0;faf95=7.266e-05;faf99=7.27e-05;non_neuro_faf95_afr=0;non_neuro_faf99_afr=0;non_cancer_faf95_eas=0;non_cancer_faf99_eas=0;non_neuro_faf95_amr=0;non_neuro_faf99_amr=0;non_topmed_faf95_sas=0;non_topmed_faf99_sas=0;controls_faf95_nfe=9.344e-05;controls_faf99_nfe=9.303e-05;non_cancer_faf95_afr=0;non_cancer_faf99_afr=0;non_cancer_faf95_amr=0;non_cancer_faf99_amr=0;non_topmed_faf95=7.178e-05;non_topmed_faf99=7.179e-05;non_neuro_faf95_nfe=0.00016851;non_neuro_faf99_nfe=0.00016761;non_neuro_faf95=7.201e-05;non_neuro_faf99=7.175e-05;non_topmed_faf95_nfe=0.00015709;non_topmed_faf99_nfe=0.00015694;controls_faf95_eas=0;controls_faf99_eas=0;controls_faf95_sas=0;controls_faf99_sas=0;faf95_nfe=0.00016146;faf99_nfe=0.00016119;non_topmed_faf95_eas=0;non_topmed_faf99_eas=0;controls_faf95_amr=0;controls_faf99_amr=0;non_neuro_faf95_eas=0;non_neuro_faf99_eas=0;non_cancer_faf95_nfe=0.00016232;non_cancer_faf99_nfe=0.00016274;non_cancer_faf95=7.019e-05;non_cancer_faf99=7.011e-05;non_cancer_faf95_sas=0;non_cancer_faf99_sas=0;non_topmed_faf95_afr=0;non_topmed_faf99_afr=0;controls_faf95=3.662e-05;controls_faf99=3.583e-05;popmax=nfe;AC_popmax=26;AN_popmax=112452;AF_popmax=0.00023121;nhomalt_popmax=0;age_hist_het_bin_freq=0|1|1|1|0|3|1|0|1|3;age_hist_het_n_smaller=3;age_hist_het_n_larger=1;age_hist_hom_bin_freq=0|0|0|0|0|0|0|0|0|0;age_hist_hom_n_smaller=0;age_hist_hom_n_larger=0;non_topmed_popmax=nfe;non_topmed_AC_popmax=25;non_topmed_AN_popmax=110366;non_topmed_AF_popmax=0.000226519;non_topmed_nhomalt_popmax=0;non_neuro_popmax=nfe;non_neuro_AC_popmax=22;non_neuro_AN_popmax=88366;non_neuro_AF_popmax=0.000248965;non_neuro_nhomalt_popmax=0;non_cancer_popmax=nfe;non_cancer_AC_popmax=24;non_cancer_AN_popmax=101636;non_cancer_AF_popmax=0.000236137;non_cancer_nhomalt_popmax=0;controls_popmax=nfe;controls_AC_popmax=8;controls_AN_popmax=42590;controls_AF_popmax=0.000187838;controls_nhomalt_popmax=0;vep=A|intron_variant|MODIFIER|TBC1D24|ENSG00000162065|Transcript|ENST00000293970|protein_coding||6/7|ENST00000293970.5:c.1302+41T>A|||||||rs370235069|1||1||SNV|1|HGNC|29203|YES|||CCDS55980.1|ENSP00000293970|Q9ULP9|H3BV07&H3BNU1|UPI000041A97A|1||||||A:0||||||A:0|A:0.0005|A:0|A:7.439e-05|A:0|A:7.477e-05|A:0|A:0|A:0.0001354|A:0||||||||||||,A|intron_variant|MODIFIER|TBC1D24|ENSG00000162065|Transcript|ENST00000434757|protein_coding||5/6|ENST00000434757.2:c.1302+41T>A|||||||rs370235069|1||1||SNV|1|HGNC|29203||||CCDS55980.1|ENSP00000390106|Q9ULP9|H3BV07&H3BNU1|UPI000041A97A|1||||||A:0||||||A:0|A:0.0005|A:0|A:7.439e-05|A:0|A:7.477e-05|A:0|A:0|A:0.0001354|A:0||||||||||||,A|downstream_gene_variant|MODIFIER|TBC1D24|ENSG00000162065|Transcript|ENST00000562105|protein_coding||||||||||rs370235069|1|3662|1|cds_end_NF|SNV|1|HGNC|29203|||||ENSP00000457896||H3BV07|UPI0002466D00|1||||||A:0||||||A:0|A:0.0005|A:0|A:7.439e-05|A:0|A:7.477e-05|A:0|A:0|A:0.0001354|A:0||||||||||||,A|intron_variant|MODIFIER|RP11-20I23.1|ENSG00000260272|Transcript|ENST00000564543|protein_coding||1/2|ENST00000564543.1:c.965+2858T>A|||||||rs370235069|1||1||SNV|1|Clone_based_vega_gene||YES||||ENSP00000455547||H3BV07&H3BQ06|UPI0002466D02|||||||A:0||||||A:0|A:0.0005|A:0|A:7.439e-05|A:0|A:7.477e-05|A:0|A:0|A:0.0001354|A:0||||||||||||,A|intron_variant|MODIFIER|TBC1D24|ENSG00000162065|Transcript|ENST00000564879|protein_coding||2/3|ENST00000564879.1:c.171+41T>A|||||||rs370235069|1||1|cds_start_NF|SNV|1|HGNC|29203|||||ENSP00000457266||H3BTP5&H3BNU1|UPI0002466D01|1||||||A:0||||||A:0|A:0.0005|A:0|A:7.439e-05|A:0|A:7.477e-05|A:0|A:0|A:0.0001354|A:0||||||||||||,A|intron_variant|MODIFIER|TBC1D24|ENSG00000162065|Transcript|ENST00000567020|protein_coding||5/6|ENST00000567020.1:c.1284+41T>A|||||||rs370235069|1||1||SNV|1|HGNC|29203||||CCDS42107.1|ENSP00000454408|Q9ULP9|H3BV07&H3BNU1|UPI000068F51B|1||||||A:0||||||A:0|A:0.0005|A:0|A:7.439e-05|A:0|A:7.477e-05|A:0|A:0|A:0.0001354|A:0||||||||||||,A|upstream_gene_variant|MODIFIER|TBC1D24|ENSG00000162065|Transcript|ENST00000569874|nonsense_mediated_decay||||||||||rs370235069|1|928|1|cds_start_NF|SNV|1|HGNC|29203|||||ENSP00000455005||H3BNU1|UPI0000E025AC|1||||||A:0||||||A:0|A:0.0005|A:0|A:7.439e-05|A:0|A:7.477e-05|A:0|A:0|A:0.0001354|A:0||||||||||||", for input source: /datadrive2/01_Mutect2/02_GetPileupSummaries/exome_site/gnomad.exomes.r2.1.1.sites_withchr.vcf.gz
        at htsjdk.variant.vcf.AbstractVCFCodec.generateException(AbstractVCFCodec.java:883)
        at htsjdk.variant.vcf.AbstractVCFCodec.parseInfo(AbstractVCFCodec.java:515)
        at htsjdk.variant.vcf.AbstractVCFCodec.parseVCFLine(AbstractVCFCodec.java:428)
        at htsjdk.variant.vcf.AbstractVCFCodec.decodeLine(AbstractVCFCodec.java:384)
        at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:328)
        at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:48)
        at htsjdk.tribble.TabixFeatureReader$FeatureIterator.readNextRecord(TabixFeatureReader.java:173)
        at htsjdk.tribble.TabixFeatureReader$FeatureIterator.next(TabixFeatureReader.java:205)
        at htsjdk.tribble.TabixFeatureReader$FeatureIterator.next(TabixFeatureReader.java:149)
        at org.broadinstitute.hellbender.engine.FeatureCache.fill(FeatureCache.java:142)
        at org.broadinstitute.hellbender.engine.FeatureDataSource.refillQueryCache(FeatureDataSource.java:568)
        at org.broadinstitute.hellbender.engine.FeatureDataSource.queryAndPrefetch(FeatureDataSource.java:536)
        at org.broadinstitute.hellbender.engine.FeatureManager.getFeatures(FeatureManager.java:352)
        at org.broadinstitute.hellbender.engine.FeatureContext.getValues(FeatureContext.java:173)
        at org.broadinstitute.hellbender.engine.FeatureContext.getValues(FeatureContext.java:125)
        at org.broadinstitute.hellbender.tools.walkers.contamination.GetPileupSummaries.apply(GetPileupSummaries.java:192)
        at org.broadinstitute.hellbender.engine.LocusWalker.lambda$traverse$0(LocusWalker.java:162)
        at java.base/java.util.Iterator.forEachRemaining(Iterator.java:133)
        at org.broadinstitute.hellbender.engine.LocusWalker.traverse(LocusWalker.java:160)
        at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1049)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:140)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)
        at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
        at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
        at org.broadinstitute.hellbender.Main.main(Main.java:289)

I have many sample sets consisting of a tumor and a control ones. Some samples have no error at the step but the other many samples have a same error with different line number of the malformed vcf. But the input vcf, that the gatk tool said as malformed one, was same at every analysis. The input vcf was originally download from gnomad v2.1 "All chromosomes sites VCF" of "Exomes" at https://gnomad.broadinstitute.org/downloads and then modified by "bcftools annotate --rename-chrs" for change chromosome name because I use non-standard reference (mixed all chromosomes from hg19 and hs37d5cs.fa). And the input bam files were checked by "picard ValidateSamFile" and have no error. And also the bams are exposed with "gatk Mutect2" and have no error as result of the step. How do I do to solve it?