About snp_pileup --pseudo-snps

[Jingjiao-ma]

hello~ About the arguments pseudo-snps ,How much should it be appropriate for WGS，WES and targeted cancer gene panels？

[veseshan]

For the snp-pileup I use 100 since insert sizes are usually larger than 100. Then use snp.nbhd in preProcSample to space them wider for WGS (say 500) than for WES (250) and targeted panel (150).

[Jingjiao-ma]

Thanks for reply. I set snp.nbhd=100, I think Facets choose a SNP sites every 100 point (like chrom1:100,chrom1:200,chrom1:300 ...),but the start and end from the cncf are not the multiplier of 100. Do I understand the wrong way？

[veseshan]

It only says that the on average one locus every interval of width snp.nbhd (withing the target regions) will be used for analysis. The locations of the loci come from the VCF file and pseudo-snps added to fill in sparse regions.

[kobejamescurry]

here "insert size" means the fragment length? for example PE150 PE200, is the insert size you are saying 150 and 200?