
woodword
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Latest activity by woodword-
woodword created a post,
RNAseq short variant discovery pipline has the unused interval file
Today when I checked the RNAseq short variant discovery pipline (https://github.com/gatk-workflows/gatk3-4-rnaseq-germline-snps-indels/blob/master/rna-germline-variant-calling.wdl ) I found task S...
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woodword commented,
I don't think MergeSamFiles takes a bam file list as an argument, so probably you have to program and run the command by some languages such as R, python, shell or WDL
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woodword commented,
Maybe this will help you: https://gatk.broadinstitute.org/hc/en-us/articles/360035890711-GRCh37-hg19-b37-humanG1Kv37-Human-Reference-Discrepancies#comparison In addition you should read this: For t...
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woodword commented,
Some of GATK tools use multi-threads, but most don't. Usually user should split their interval files and process each of them simultaneously to speed up. Once all intervals are finished, one can me...
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woodword commented,
You mean this ? gatk MergeSamFiles -I 1.bam -I 2.bam -I 3.bam -I 4.bam -I 5.bam -I 6.bam -I 7.bam -I 8.bam -I 9.bam -I 10.bam -I 11.bam -I 12.bam -I 13.bam -I 14.bam -I 15.bam -I 16.bam -I 17.bam -...
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woodword commented,
Try this https://console.cloud.google.com/storage/browser/gcp-public-data--broad-references/hg38
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woodword commented,
You can try 'bcftools norm -m+both, for more detail check https://samtools.github.io/bcftools/bcftools.html#norm
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woodword commented,
Maybe these two posts could give your some clues https://gatk.broadinstitute.org/hc/en-us/articles/360047216371-DepthPerAlleleBySamplehttps://gatk.broadinstitute.org/hc/en-us/articles/36004721787...
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woodword commented,
unmapped.BAM is the output of "RevertSam" task in the RNA germline calling workflow. It has nothing to do with STAR. Since most of the people use fastq files as the input of RNA germline calling wo...
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woodword commented,
Try to downgrade GATK to 4.1.3.0