Can you please provide
a) GATK version used : 4.1.7
b) Exact GATK commands used: ./gatk --java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true' HaplotypeCaller -R Jatropa.fna -I Sample_A_SplitNcigar.bam -O Sample_A_1_output.g.vcf.gz -ERC GVCF
c) The entire error log if applicable.  ALT present as a <NON_REF> in all 4 output files. Actually i am following "BaseRecalibrator without a set of known SNPs" thread as there is no SNPs for jatropha. since the files comes in this format when  i am trying to run "hard-filtering" output files are empty.

I am new to GATK so i am following threads but here i am stuck. Can some one guide me how i can get vcf file to run "BaseRecalibrator."

Please check below small part of  HaplotypeCaller output:

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 20
NW_012124042.1 1 . C <NON_REF> . . END=25644 GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0
NW_012124043.1 1 . C <NON_REF> . . END=3153 GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0
NW_012124043.1 3154 . A <NON_REF> . . END=3160 GT:DP:GQ:MIN_DP:PL 0/0:1:3:1:0,3,39
NW_012124043.1 3161 . T <NON_REF> . . END=3161 GT:DP:GQ:MIN_DP:PL 0/0:1:0:1:0,0,0
NW_012124043.1 3162 . T <NON_REF> . . END=3209 GT:DP:GQ:MIN_DP:PL 0/0:1:3:1:0,3,43
NW_012124043.1 3210 . G <NON_REF> . . END=3243 GT:DP:GQ:MIN_DP:PL 0/0:2:6:2:0,6,49
NW_012124043.1 3244 . A <NON_REF> . . END=3272 GT:DP:GQ:MIN_DP:PL 0/0:1:3:1:0,3,44
NW_012124043.1 3273 . T <NON_REF> . . END=3273 GT:DP:GQ:MIN_DP:PL 0/0:1:0:1:0,0,0
NW_012124043.1 3274 . A <NON_REF> . . END=3298 GT:DP:GQ:MIN_DP:PL 0/0:1:3:1:0,3,44
NW_012124043.1 3299 . G <NON_REF> . . END=24659 GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0
NW_012124044.1 1 . A <NON_REF> . . END=624 GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0
NW_012124044.1 625 . C <NON_REF> . . END=680 GT:DP:GQ:MIN_DP:PL 0/0:1:3:1:0,3,20
NW_012124044.1 681 . G <NON_REF> . . END=715 GT:DP:GQ:MIN_DP:PL 0/0:2:6:2:0,6,49
NW_012124044.1 716 . A <NON_REF> . . END=768 GT:DP:GQ:MIN_DP:PL 0/0:1:3:1:0,3,35
NW_012124044.1 769 . C <NON_REF> . . END=30828 GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0
NW_012124045.1 1 . G <NON_REF> . . END=27954 GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0
NW_012124045.1 27955 . T <NON_REF> . . END=27955 GT:DP:GQ:MIN_DP:PL 0/0:1:3:1:0,3,38
NW_012124045.1 27956 . C <NON_REF> . . END=27964 GT:DP:GQ:MIN_DP:PL 0/0:1:0:1:0,0,0
NW_012124045.1 27965 . T <NON_REF> . . END=27965 GT:DP:GQ:MIN_DP:PL 0/0:1:3:1:0,3,44
NW_012124045.1 27966 . C <NON_REF> . . END=27967 GT:DP:GQ:MIN_DP:PL 0/0:1:0:1:0,0,0
NW_012124045.1 27968 . T <NON_REF> . . END=27970 GT:DP:GQ:MIN_DP:PL 0/0:1:3:1:0,3,45
NW_012124045.1 27971 . T <NON_REF> . . END=27974 GT:DP:GQ:MIN_DP:PL 0/0:1:0:1:0,0,0
NW_012124045.1 27975 . T <NON_REF> . . END=27978 GT:DP:GQ:MIN_DP:PL 0/0:1:3:1:0,3,45
NW_012124045.1 27979 . C <NON_REF> . . END=27983 GT:DP:GQ:MIN_DP:PL 0/0:1:0:1:0,0,0
NW_012124045.1 27984 . C <NON_REF> . . END=27984 GT:DP:GQ:MIN_DP:PL 0/0:1:3:1:0,3,45
NW_012124045.1 27985 . T <NON_REF> . . END=27989 GT:DP:GQ:MIN_DP:PL 0/0:1:0:1:0,0,0
NW_012124045.1 27990 . T <NON_REF> . . END=27993 GT:DP:GQ:MIN_DP:PL 0/0:1:3:1:0,3,45
NW_012124045.1 27994 . C <NON_REF> . . END=27994 GT:DP:GQ:MIN_DP:PL 0/0:1:0:1:0,0,0

Thanks