Mark Godek
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Activity overview
Latest activity by Mark Godek-
Mark Godek commented,
I have a similar issue. INFO column of VCF only has counts of ALT allele, but haplotype caller called the position as heterozygous. Examining the BAM verified all reads were for ALT allele. Any ide...
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Mark Godek commented,
I found a post on Biostars on excluding based on SelectVariants and it seems to have worked when I tried it. gatk SelectVariants -R /mnt/data/rbueno/ref_genomes/human/BWA-MEM/b37_decoys/hs37d5.fa -...
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Mark Godek commented,
Hi Genevieve-Brandt-she-her, I tried VariantFiltration and it works, however it throws a warning as it is running. I'm not sure if this is a big deal because it does create the output VCF and adds ...
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Mark Godek commented,
Hi Genevieve-Brandt-she-her, I'm using SelectVariants because it was recommended under heading 6 of the Variant Call Format page of the GATK website. Actually, rereading it, it does say it works on...
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Mark Godek commented,
Hi danilovkiri, I know about how 1000Genomes was generated, but I can't find any info about the 1000G_phase1.snps.high_confidence.hg38.vcf.gz file on the IGSR website or FTP server. Is this just t...
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Mark Godek commented,
I'm following the GATK best practices for somatic and germline SNP discovery. For cohort command through bash, do you mean using gatk GenotypeGVCFs to call variants of a cohort from a genomics DB? ...
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Mark Godek created a post,
SelectVariants JEXL expression works in somatic matched pair but not germline cohort
Running on one of the matched pairs used in this cohort (command below) works fine. When I run it on the jointcalled cohort, it creates the filtered VCF and index file, but produces an error. Do I ...
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Mark Godek commented,
12:70747010 was the last successfully annotated position. 12:70747693 causes the error. 12:70753674 would be the next position to be annotated if the exception did not occur. 12 70747010 . G A 84.7...
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Mark Godek commented,
I tried renaming the chromosomes in the filtered variants before annotating and using an hg19 reference and it's still complaining about contigs. I think it annotated fine with the b37 naming, I'm ...
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Mark Godek commented,
Thanks. Yeah, I imagined it had something to do with the data sources. I'm using b37 for everything but the annotation sources in the broad bundle only have hg19 and hg38. I was hoping it would be ...