Siddharth Prakash
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Latest activity by Siddharth Prakash-
Siddharth Prakash commented,
I am stuck for two reasons: 1. When I ran this command 6 months ago it worked just fine. I used bwa 0.7.16 instead of 0.7.17 then. I just reran the same .fastq files that I had successfully aligned...
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Siddharth Prakash commented,
Yes, my output is interleaved paired-end. Output is from cutadapt 3.1.
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Siddharth Prakash commented,
Hi Genevieve, Yes, I reran the pipeline and checked the preprocessed bams. They all look the same as what I posted. I'm calling bwa/0.7.17. Any suggestions?
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Siddharth Prakash commented,
I went back to my alignment and preprocessing steps and found no errors. I confirmed that my reference hs37d5 is consistent. This is my workflow: module use /work2/03437/sprakash/lonestar/apps/modu...
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Siddharth Prakash commented,
Follow up: I checked the .bam file that I used as target for the previous command in igv. This .bam was created from paired end fastq files using the recommended pipeline in GATK 4.1.8, which I had...
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Siddharth Prakash commented,
It's not what I'm looking for. My vcfs are truly empty, with just a header. My command: java -Xmx4g -jar ${GATK_DIR}/gatk-package-4.1.8.0-local.jar HaplotypeCaller -ERC GVCF -R $REF -I ${BAMDIR}/51...
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Siddharth Prakash commented,
Hi! We are having the same issue with HC and Mutect2. I tried to follow this thread but never saw how you resolved the issue. Can someone repeat the answer or point me in the right direction?
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Siddharth Prakash created a post,
Problems with FastQtoSAM
AnsweredHi! I'm running FastQtoSAM on GATK 4.1.8. I submitted 65 parallel tasks and received 19 errors. Why are some but not all of my FastQ files triggering errors? What do the errors mean? Can I avoid th...