kvn95ss
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Activity overview
Latest activity by kvn95ss-
kvn95ss created a post,
GATK Haplotypecaller is calling Heterozygous variant, but bamout doesn't reflect the read frequencies in gvcf file
REQUIRED for all errors and issues: a) GATK version used: 4.2.6.1 and 4.3.0.0b) Exact command used: gatk HaplotypeCaller -R "$ref_hg38" -I input.bam -L twist.bed -ERC GVCF -ip 50 -O test_latest.gvc...
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kvn95ss commented,
Hay, When using hg38, were the alternate contigs retained or removed? If they were retained, you could try removing them (or using a hg38 no alt reference) and then check. Is the data generated via...
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kvn95ss commented,
Any updates on this? Am I doing something wrong?
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kvn95ss created a post,
GatherVCFs error - provider not installed
I am trying to create a panel of normal following this guide - https://gatk.broadinstitute.org/hc/en-us/articles/360035531132--How-to-Call-somatic-mutations-using-GATK4-Mutect2 I have split the gen...
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kvn95ss commented,
You can try writing the bam list into a file, then use parallel -a to use that list as input For Ex. ls *.sorted.bam > input_list # Not the best way to be frankfind $PWD -name "*.sorted.bam" > inpu...
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kvn95ss commented,
You have got it correct. AFAIK genomicsDB only allows samples to be updated, but doesn't support removal / replacement of samples. A new genomicsDB would have to be created. Do check out the Rebloc...
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kvn95ss commented,
Just a note, you could run the haplotype caller again with the switch --bam-output to understand which reads were used as evidence for the variant calling.
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kvn95ss commented,
Hello, It might be a good option to use reblockgvcf on the WGS samples. For ex. the size of a single WGS gvcf went from ~13GB to ~900 MB. This helped a ton with reduced memory requirement, which in...
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kvn95ss commented,
jfarrell and Genevieve Brandt (she/her) using normal gvcf, creating genomics db using genomicsdb and genotypegvcf used to take ~24 hours (around 1.9k samples, split across each chr, while chr1 and ...
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kvn95ss commented,
Sorry for bumping an old thread, but I am facing similar problems with the memory requirements and inability to scatter across multiple smaller intervals due to server hardware limitations. I was g...