Damian Fermin
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Activity overview
Latest activity by Damian Fermin-
Damian Fermin created a post,
Picard CollectWGSMetrics vs QualiMap vs samtools stats
REQUIRED for all errors and issues: a) GATK version used: v4.3.0.0b) Exact command used: gatk CollectWgsMetrics --MAX_RECORDS_IN_RAM 10000000 -R $FASTA -I $BAM -O $OUT I'm having trouble reconcili...
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Damian Fermin created a post,
Unable to run Picard GtcToVcf
I have a GTC file I'd like to convert to a VCF file using Picard's GtcToVcf funcionality. a) Picard version: 2.27.4-SNAPSHOT b) Exact command: java -Xmx32g -jar /usr/local/bin/picard.jar GtcToVcf \...
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Damian Fermin created a post,
What is the correct step? VQSR and CNNScoreVariants?
AnsweredI think this should be an easy one so I apologize if it's a stupid question. I'm confused from reading the Best practices workflow for Germline short variant discovery. I am trying to get a set of ...
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Damian Fermin created a post,
Should decoy chromosomes be dropped at HaplotyeCaller Step?
Hi I am analyzing ~600 30X WGS samples using GATK 4.1.8.0 and I've finally reached the stage where I can run my recalibrated BAM files through HaplotypeCaller. I know I can speed the process up via...
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Damian Fermin commented,
So I looked at the BAM files for the sites with the stray variants. They are definitely getting a lot of reads supporting their call (some in excess of 100). Extracting about 20 of these aligned...
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Damian Fermin commented,
Hi Derek Thanks for getting back to me. I've checked the BAM files for each patient looking at the average read depth of the gene SRY. It's on the Y chromosome and should not have read counts for...
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Damian Fermin created a post,
Calling variants on chromosome Y
Hello I'm trying to use GATK 4.1 to analyze WGS data I have.At this point I'm only testing and optimizing my pipeline so I am only working with 4 samples (2 males and 2 females). I've followed the ...