User: jtwalker

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jtwalker10
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Posts by jtwalker

<prev • 15 results • page 1 of 2 • next >
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VCF format: what does AD 1,0 denote?
... I'm looking at one of my VCF files and I noticed that allele depth (AD) isn't just one number, but rather two values seperated by a comma e.g.: GT:AD:DP:GQ:PL 0/0:**1,0**:1:3:0,3,27 The [GATK doc](https://gatkforums.broadinstitute.org/gatk/discussion/1268/what-is-a-vcf-and-how-should-i-i ...
vcf written 9 days ago by jtwalker10 • updated 9 days ago by Pierre Lindenbaum98k
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Comment: C: Badly formed genome location? GATK GenotypeGVCFs
... They were all created with the same method, namely GATK's HaplotypeCaller ...
written 15 days ago by jtwalker10
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Comment: C: Badly formed genome location? GATK GenotypeGVCFs
... cut -f 1 S1097.g.vcf | grep -F 024218.1 | uniq ##contig= NC_024218.1 I have over a thousand g.vcfs. Could it be that one of them contains a malformed contig name causing the problem? ...
written 15 days ago by jtwalker10
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Comment: C: Badly formed genome location? GATK GenotypeGVCFs
... GCF.dict:@SQ SN:NC_024218.1 LN:77392008 M5:0ad5ac74565c0b48329eec6020994b16 UR:file:/Users/lukehoekstra/GenomeAnalysisTK-3.7/GCF.fna GCF.fna.fai:NC_024218.1 77392008 125 80 81 ...
written 15 days ago by jtwalker10
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Badly formed genome location? GATK GenotypeGVCFs
... I'm trying to genotype >1000 samples using the GATK pipeline. I've already created gVCFs for my samples, but when attempting to use GATK's GenotypeGVCFs tool, I get the following error BiasBySample values to calculate strand bias annotation values. If no sample has the SB genotype annotatio ...
gatk joint genotyping written 16 days ago by jtwalker10
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Comment: C: Regarding vcf output
... You might also consider filtering on QD rather than QUAL and DP: https://software.broadinstitute.org/gatk/documentation/article.php?id=6925 ...
written 8 weeks ago by jtwalker10
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Comment: C: GATK variantFiltration unexpected behaviour?
... It didn't give me an error, but I'll try that now. Thanks! ...
written 9 weeks ago by jtwalker10
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Comment: C: GATK variantFiltration unexpected behaviour?
... A line from the VCF: NC_024218.1 10250670 . C T 61.23 PASS AC=2;AF=0.333;AN=6;DP=75;ExcessHet=1.0474;FS=0.000;MLEAC=2;MLEAF=0.333;MQ=10.95;QD=30.62;SOR=0.693 GT:AD:DP:GQ:PGT:PID:PL 0/0:6,0:6:18:.:.:0,18,230 ./.:1,0:1:.:.:.:0,0,0 1/1:0,2:2:6:1|1:10250670_C_T:90,6,0 ./.:2,0:2:.:.:.:0,0,0 ./.:10,0 ...
written 9 weeks ago by jtwalker10
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Comment: C: Filtering on MAF using the GATK?
... That's good to know. I appreciate the answer! Thanks ...
written 9 weeks ago by jtwalker10
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GATK variantFiltration unexpected behaviour?
... Hello, I'm trying to use the GATK to hard filter variants (I'm using a non-model organism, so variant re calibration isn't possible), but, while I'm following the GATK website's tutorial (https://gatkforums.broadinstitute.org/gatk/discussion/2806/howto-apply-hard-filters-to-a-call-set), I haven't a ...
gatk variant filtration snp written 9 weeks ago by jtwalker10

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