poisonalien/varscan_accessories

accessory scripts for processing varscan somatic/copynumber outputs.

Command line accessory scripts for processing varscan somatic/copynumber outputs.

vs_format_converter.py converts varscan somatic output from vcf to snp and vice-versa

vs_indel_to_annovar.py converts varscan somatic indels to annovar input.

dnaCopyScan.R Takes output from varscan copynumber command (.copynumber) and performs CBS segmentation.

varscan_accessories's Issues

SNP and copy number conversion?

Hi,

Does these scripts also work when converting copy number findings from VarScan? I see from the other, well-used thread that they work for indels and SNPs at least.

Thanks!

License?

Hi,

Your vs_format_converter.py script looks very useful, thank you for sharing it. However, because you haven't stated a license for it, it's not actual legal for anyone to use it.

Please can you add license information to your repo so that I can give your script a try? This site makes it easy to choose the right one for you.

Thanks,
Luke

A bug line 179

Thank you for the very useful script! There is a bug:

line 179 dp42 = nIp[15] + ',' + nIp[16] + ',' + nIp[17] + ',' + nIp[19]

should be dp42 = nIp[15] + ',' + nIp[16] + ',' + nIp[17] + ',' + nIp[18]