varscan2
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Jeltje
Scripts to run copynumber variation calls on tumor and normal BAM files using Varscan2
I'm getting an [error trying to feed `Varscan2.3.9` data into `SnpEff`](https://github.com/pcingola/SnpEff/issues/267#issuecomment-736928876). The developer says this is because the `ID` column is missing.
Hello , I want to known if the centromeres.bed is normal? Thank you ! chr1 121535434 124535434 chr2 92326171 95326171 chr3 90504854 93504854 chr4 49660117 52660117 chr5 46405641 49405641 chr6...
`/var/spool/cwl` is not part of the CWL v1.x standards. See https://github.com/common-workflow-language/common-workflow-language/issues/674 for a discussion.
This is a more flexible way to check the sorting order of a BAM file.
Compare chromosomes listed in the bed, genome, and bam files
$ bcftools concat -O v -o varscan.indel_merged.vcf chr1.recode.vcf chr2.recode.vcf chr3.recode.vcf chr4.recode.vcf chr5.recode.vcf chr6.recode.vcf chr7.recode.vcf chr8.recode.vcf chr9.recode.vcf chr10.recode.vcf chr11.recode.vcf chr12.recode.vcf chr13.recode.vcf chr14.recode.vcf chr15.recode.vcf chr16.recode.vcf chr17.recode.vcf chr18.recode.vcf chr19.recode.vcf chr20.recode.vcf chr21.recode.vcf chr22.recode.vcf chrX.recode.vcf...
