Calls somatic SNVs, indels, and allelic copy number jointly across multiple samples from the same patient. These can be standard tumor/normal pair, longitudinal samples, primary/met, etc. Can also be used for tumor only calling, ideally with a high tumor content and a low tumor content sample.
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runNormalMetrics output - chromosomes represented as numbers (chrN+1) #7
When I run runNormalMetrics on test bam files from 1000 genomes, the chromosomes in the 1st column of the output files were correct - 1..22, X, Y.
When I run my bam files, all chromosomes outputted as numbers - chromosome number plus 1. So chromosome 1 becomes 2, 2 becomes 3, 22 -> 23, X -> 24 and Y -> 25. Why is this?
In my reference and bam files, the first contig is mitochondrial chromosome ( represented as M). Can it be the reason? It's not in the bed file I use as the regionsFile. I also tried to subset the bam files to remove M contigs before running runNormalMetrics (with samtools view -L), but it didn't change the output. (Well, it actually was not removed from the header.)
I have to mention that my bam files and reference (hg19) originally have "chr" prefix in contigs labels. I modified both the reference and bam files removing this prefix. Will gvm eventually support this prefix? Is there a better way to deal with such files?
When I run runNormalMetrics on test bam files from 1000 genomes, the chromosomes in the 1st column of the output files were correct - 1..22, X, Y.
When I run my bam files, all chromosomes outputted as numbers - chromosome number plus 1. So chromosome 1 becomes 2, 2 becomes 3, 22 -> 23, X -> 24 and Y -> 25. Why is this?
In my reference and bam files, the first contig is mitochondrial chromosome ( represented as M). Can it be the reason? It's not in the bed file I use as the regionsFile. I also tried to subset the bam files to remove M contigs before running runNormalMetrics (with samtools view -L), but it didn't change the output. (Well, it actually was not removed from the header.)
I have to mention that my bam files and reference (hg19) originally have "chr" prefix in contigs labels. I modified both the reference and bam files removing this prefix. Will gvm eventually support this prefix? Is there a better way to deal with such files?
Thanks