User: MMa
MMa • 210
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Posts by MMa
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... The docs for the current versions of pindel states depth is the same I'd get from `samtools depth`. ...
written 9 weeks ago by
MMa • 210
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... I got from our collaborator some pindel output and the BAM files that is used as pindel input. Unfortunately, they used an older of version of pindel (before approximately 0.2.4u) that doesn't record total depth at breakpoint (i.e. the DP field in VCF). While our collaborator's standard practice is ...
written 9 weeks ago by
MMa • 210
• updated
9 weeks ago by
Pierre Lindenbaum ♦ 98k
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... If you did that successfully on a different file yesterday, then check whether the smallfile.vcf you're using today have been indexed. ...
written 10 weeks ago by
MMa • 210
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... I mean the `bcftools annotate` command line. ...
written 11 weeks ago by
MMa • 210
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... What exactly was the command line you used? bcftools output gzipped vcf by default, so try renaming OCT1.genome_min.vcf to OCT1.genome_min.vcf.gz and retry. ...
written 11 weeks ago by
MMa • 210
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... It's actually more of `bcftools annotate -a largefile.vcf -c [comma separated of INFO tags you want to transfer in the form of DST_TAG:=SRC_TAG] smallfile.vcf` ...
written 11 weeks ago by
MMa • 210
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... I've been trying to find a python driver for VCF that allows me to search the VCF by one or more IDs without me writing loops, but I haven't found any that doesn't use databases. Does parsers like that exist, or do I really need to use a database for that? ...
written 3 months ago by
MMa • 210
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... library (vcfR)
MT12VCF <- function (inputFile, outFile){
inputDF <- read.delim (inputFile, stringsAsFactors=F)
if ((length(unique(inputDF$normal_name)) > 1) ||
(length(unique(inputDF$tumor_name)) > 1)){
stop ("This function assumes ...
written 3 months ago by
MMa • 210
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... Since the comment above implied there isn't, eventually I wrote one in R that should provide all the fields that `-vcf` emits; but since the raw MuTect text out doesn't give out the raw DP, the DP is derived as the sum of the two ADs.
This script is also based on the assumption that MuTect1 only em ...
written 3 months ago by
MMa • 210
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... I have received some MuTect v1 text outputs from our collaborator. While I can probably write scripts that can convert the output into VCF, are there software out there that does this? R, Perl or Python are fine. ...
written 3 months ago by
MMa • 210
Latest awards to MMa
Teacher
4 months ago,
created an answer with at least 3 up-votes.
For A: Different results with edgeR when adding gene symbols
Scholar
4 months ago,
created an answer that has been accepted.
For C: I get the same modules but different number of genes WGCNA
Scholar
4 months ago,
created an answer that has been accepted.
For C: I get the same modules but different number of genes WGCNA
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