
Wiebe Kooistra
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Activity overview
Latest activity by Wiebe Kooistra-
Wiebe Kooistra created a post,
GenotypeGVCFs too many alleles
Hi, I have an issue that I am missing a location in my final VCF file. I have over 1500 samples, that have been sequenced with Illumina, and I am using HaplotypeCaller, GenomicsDB, and GenotypeGVCF...
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Wiebe Kooistra commented,
Hey Laura Gauthier Thanks for looking into this :). Wiebe
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Wiebe Kooistra created a post,
VariantFiltration filtering all SNPs for all samples to missing
REQUIRED for all errors and issues:a) GATK version used: 4.4.0.0b) Exact command used: gatk VariantFiltration -R ${reference} -V ${vcf} \ --genotype-filter-name 'GQ_20' --genotype-...
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Wiebe Kooistra commented,
Hey, Sure. Here is the VCF output line: SL4.0ch11 25548831 . T C,A 4.09785e+06 PASS AC=1,0;AF=0.523,0.006162;AN=2;BaseQRankSum=-0.295;DP=257674;ExcessHet=-0;FS=0;InbreedingCoeff=0.6408;MLEAC=819,8;...
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Wiebe Kooistra commented,
Hi Genevieve Brandt (she/her) I did read about the local realignment. There are 173 ArtificialHaplotypeRG's marked sequences. That the numbers don't add up I understand, I was just wondering why my...
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Wiebe Kooistra created a post,
ArtificialHaplotypeRG makes variant heterozygous
AnsweredDear GATK, Why do I see the Artificial Haplotype RG add more heterozygosity? In the top part we have the bam file after using HaplotypeCaller with the option --bamfile. In the lower part there is ...
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Wiebe Kooistra commented,
Hi Pamela Bretscher, I do not have a bamout image for this. The command that was run: gatk HaplotypeCaller -R ref.fasta -ERC GVCF --dont-use-soft-clipped-bases true --do-not-run-physical-phasing tr...
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Wiebe Kooistra commented,
Hey Pamela Bretscher The full GVCF line is: Ls_98839 100 . A <NON_REF> . . END=100 GT:DP:GQ:MIN_DP:PL 0/0:2007:0:2007:0,0,0 The stack trace is: 15:11:08.430 INFO NativeLibraryLoader - Loading libgk...
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Wiebe Kooistra commented,
Hey Pamela, For the GVCF file do you want to see multiple lines or just of the SNP location that I am expecting? For the full stack trace? Do you mean the output HaplotypeCaller is giving when runn...
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Wiebe Kooistra commented,
Hey Pamela Bretscher, I am using HaplotypeCaller and not Mutect2, but I did change --pruning-lod-threshold to the same levels as the gentlemen did (1.3, 0.5 and 0.1). The genotype and the GQ score ...