woodword
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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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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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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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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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Try this https://console.cloud.google.com/storage/browser/gcp-public-data--broad-references/hg38
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You can try 'bcftools norm -m+both, for more detail check https://samtools.github.io/bcftools/bcftools.html#norm
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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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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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Try to downgrade GATK to 4.1.3.0
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I am not sure where the problem is. I've tried the every version of GATK ( 4.1.4.0 to 4.1.9.0) with the same data and resource files. The issue disappeared when I ran 4.1.4.0 and 4.1.4.1. GATK 4.1....