User: abbysue

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abbysue10
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7 months, 2 weeks ago
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7 months, 3 weeks ago
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Posts by abbysue

<prev • 7 results • page 1 of 1 • next >
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Comment: C: BWA index getting killed
... I realized that recently, stupid mistake by me. Thanks!! ...
written 7 months ago by abbysue10
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BWA index getting killed
... I'm trying to index fastq files using this command bwa index -p testbwaidx -a bwtsw test.fastq However, the process keeps getting killed after ~10 minutes despite having 53G of memory open. Here's the error message [bwa_index] Pack FASTA... Killed ...
fastq bam bwa index written 7 months ago by abbysue10 • updated 7 months ago by swbarnes27.5k
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Comment: C: Pipe SamToFastq, BWA mem not working
... Nope (this 20 character min... damn) ...
written 7 months ago by abbysue10
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Comment: C: Pipe SamToFastq, BWA mem not working
... I ended up running gatk SamToFastq -I markedadapters.bam -F f797.fastq --CLIPPING_ATTRIBUTE XT --CLIPPING_ACTION 2 --INTERLEAVE true -NON_PF true -TMP_DIR= path/hello which of course worked. I tried your command and it worked!! So should I include the " > file.fastq" blurb to get my piped ...
written 7 months ago by abbysue10
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Pipe SamToFastq, BWA mem not working
... I'm going through the GATK pipeline to realign bam files. I'm using this command line: gatk SamToFastq -I markedadapters.bam -F /dev/stdout --CLIPPING_ATTRIBUTE XT --CLIPPING_ACTION 2 --INTERLEAVE true -NON_PF true -TMP_DIR= path/hello | bwa mem -M -t 12 -p /mydata/Homo_sapiens_assembly38.fasta ...
gatk sam bwa pipe written 7 months ago by abbysue10 • updated 3 months ago by Marco Pessoa0
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Stats on WGS variant calls
... What's the best way to collect some statistics on 4 mil variants identified with GATK pipeline (and annotated with Funcotator)? I'm having trouble parsing info in the 'Funcotator' annotation since it contains several pieces of info that I want, separated by pipe characters. I want to know # of Intro ...
wgs variants written 7 months ago by abbysue10 • updated 7 months ago by reza.jabal350
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Parsing through VCF annotated by Funcotator
... I have a variant set annotated by GATK's Funcotator... creates an extra field in the VCF called "Funcotator" with several [annotations][1] separated by pipe characters. I want to get some statistics on % intronic vs exonic and missense/nonsense mutations. Is the easiest way to do this using grep? Or ...
vcf gatk annotated funcotator written 7 months ago by abbysue10 • updated 5 months ago by jonnsmith0

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