User: jtwalker

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jtwalker20
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Posts by jtwalker

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Comment: C: Speed up GATK joint genotype calling?
... I had considered this, but the gatk doc says that we'd need to have the same amount of ram available for each thread. As our ram usage is already a concern, would this still be a viable option? ...
written 26 days ago by jtwalker20
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Speed up GATK joint genotype calling?
... I'm using GATK's GenotypeGVCFs tool to jointly genotype ~1000 samples. It's my understanding that because of the genome wide annotations that are calculated, I can't speed things up by using CombineVCFs on smaller jointly called groups. Am I correct? Is there some way to speed up my joint genotypin ...
gatk joint genotyping written 26 days ago by jtwalker20
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Answer: A: Badly formed genome location? GATK GenotypeGVCFs
... Just to update this question in case anyone is having a similar problem - for some reason when I used BWA mem the output for a few of my files was malformed, which led to problems down the line. I simply realigned the files and my joint call worked. ...
written 6 weeks ago by jtwalker20
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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 10 weeks ago by jtwalker20 • updated 10 weeks ago by Pierre Lindenbaum101k
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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 10 weeks ago by jtwalker20
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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 10 weeks ago by jtwalker20
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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 10 weeks ago by jtwalker20
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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 11 weeks ago by jtwalker20
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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 4 months ago by jtwalker20
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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 4 months ago by jtwalker20

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