mk
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Hello, Isn't DP/AD being much greater than the coverage an abnormal result? Thank you
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Hi, thank you. I read the docs before posting. It explains what the parameter does. My question was why should we do this (as is done in the implementation of the best practices). Thank you.
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I have traced the source of both issues: it is the coverage plot which is generated using deeptools bamCoverage that is causing the observed slope in coverage and reporting a different (lower) coun...
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Hello David, Thank you for looking into this. It's the NCBI SARS-CoV2 reference genome (NC_045512.2). Please let me know if you need any other info.
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Hi, Thank you for looking into this. I have copied a file called mk_sample.bam to the ftp server.
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Hi, apologies, command is below. I am not running with contamination downsampling argument. gatk HaplotypeCaller \-R $ref \-I $bam \-O raw_variants.vcf \-bamout haplotypecaller_bamout.bam \-ploidy 1
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Thank you.
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Hello, apologies for the delay in my response, please see command below: bamCoverage \-p max \--bam $bam \--binSize 1 \--ignoreDuplicates \--minMappingQuality 20 \
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Hello, 1) The coverage plot is generated using deeptools bamCoverage 2) I have shared the files in a tarball called bamout_vs_vcf_dp.tar.gz, the bamout.bam file was only 2 MB so I shared the entire...
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Hi, thank you. What is shown in the images is a bigwig (coverage plot) of the bamout file (grey), with the AD from the VCF overlayed in green. There is no bam file here. Thank you.