comparing tumor WGS vs normal exome

mskcc / facets

Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.

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comparing tumor WGS vs normal exome #38

Open aanchalsharma opened 7 years ago

aanchalsharma commented 7 years ago

Hello,

I have data where the tumor samples have been sequenced for whole genome whereas the normal samples are whole exome. Can I run these samples as such with facets or should I extract exonic regions from WGS data (for tumor) and then run it or its not a good idea to run such cases at all because of the difference in coverage in case of WGS and WES? Thanks.

veseshan commented 7 years ago

You can use the data as is. If you run snp-pileup where you specify a reasonable minimum read depth for the normal (for example -r25,0) the resulting data will reduce to WES level since only loci with sufficient read counts in the normal will be written to the counts file.

Venkat