mk
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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.
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Thank you. In this post, the difference is 1 read. All other posts i have found discuss the AD being less in the VCF than the original BAM, or similar. In my case, the VCF is reporting AD almost tw...
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Hello, Isn't DP/AD being much greater than the coverage an abnormal result? Thank you