snp-pileup with -A option

[jh2663]

Hi. I've found that some of my BAM files include some anomalous read pairs so that snp-pileup returns only empty chrXX.csv.gz files. The solution would be using '-A' flag as mentioned in here : mskcc/facets#63

So, could you rewrite the script to include this option in your package? Thank you.

[dariober]

Thanks for reporting the issue. I'm travelling at the moment so I'll fix this in a few days by adding the -A option.

For the time being you can run snp-pileup on its own and pass the pileup file to cnv_facets.R (see pileup-input).

Alternatively, you can edit the script cnv_facets.R (you can find it by executing which cnv_facets.R) by replacing on line 276 'snp-pileup' with 'snp-pileup -A'. Note also that without properly paired reads, the parameter --nbhd-snp will be set to 250 instead of being set to the average insert size.

[dariober]

Hi- apologies this took so long. I uploaded to bioconda a new version of cnv_facets which implements the option --snp-count-orphans/-A. Assuming you have conda/bioconda already installed and configured, update with:

conda update cnv_facets
# Or install with
conda install cnv_facets