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3. Why does my vcf contain a genotype when there are no reads supporting it?

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
• January 11, 2021 00:13
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2. Germline
3. SelectVariants JEXL expression works in somatic matched pair but not germline cohort

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
• August 18, 2020 13:53
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3. SelectVariants JEXL expression works in somatic matched pair but not germline cohort

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
• August 18, 2020 13:41
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3. SelectVariants JEXL expression works in somatic matched pair but not germline cohort

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
• August 17, 2020 23:25
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2. Documentation Questions
3. Questions Regarding VCF Files Found in hg38 Public Resource Bundle

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
• August 17, 2020 19:23
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2. Germline
3. SelectVariants JEXL expression works in somatic matched pair but not germline cohort

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
• August 12, 2020 23:57
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2. Germline
3. Funcotator cannot complete funcotaion for variant due to alternate allele

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
• June 06, 2020 20:16
• Edited
• 0 votes

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2. Germline
3. Funcotator cannot complete funcotaion for variant due to alternate allele

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
• May 29, 2020 13:51
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3. Funcotator cannot complete funcotaion for variant due to alternate allele

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 ...

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• Mark Godek
• May 28, 2020 14:37
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• 0 votes

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2. Non-Human
3. Provider "genedb" not found when using SelectVariants & GenomicsDBImport

OK, SelectVariants works with -V gendb:///PHShome/mi313/example_familial/output/pon_db as well. The syntax with all the forward slashes was throwing me off. I thought I tried all permutations befor...

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• Mark Godek
• March 30, 2020 17:52
• 1 vote