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Tools for producing pseudo-cgh of next-generation sequencing data

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Bugfix

Line 97 of scripts/ngCGH in the upstream master is creating a truncated list, which contain only first regions of every chromosome in a bed file. This PR fixed it so...

biocyberman avatar biocyberman

regions options problem

I’ve been using ngCGH for sometime without error and I love it. However I’d like to take advantage of the –r option. I keep getting "IndexError: list index out of...

oalder avatar oalder

Add -F and -f like samtools for filtering reads

seandavi avatar seandavi

Add filter for mapping quality

seandavi avatar seandavi

Output QC metrics

For each ngCGH run, calculate QC metrics such as number of reads, mapping quality, paired-end reads, etc. Also, consider sex-ratio calculation based on sex chromosomes. Finally, calculate DLRS.

seandavi avatar seandavi

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verified publisher icon seandavi

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Tools for producing pseudo-cgh of next-generation sequencing data

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