ANGSD: Analysis of next generation Sequencing Data
Latest tar.gz version is (0.938/0.939 on github), see Change_log for changes, and download it here.
Contamination: Difference between revisions
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./angsd -i my.bam -r X: -doCounts 1 -iCounts 1 -minMapQ 30 -minQ 20 | |||
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Revision as of 12:46, 27 June 2014
Angsd can estimate contamination, but only for chromosomes that exists in one genecopy (eg chrX for males). This method requires a list of HapMap sites along with their frequency and we also recommend to discard regions with low mappability.
We have included a mappability and HapMap files for chrX these are found in the RES subfolder of the angsd source package. So if you are working with humans, and your sample is a male then you can estimate the contamination with the follow two commands.
- First we generate a binary count file for chrX for a single BAM file (ANGSD cprogram)
- Then we do a fisher test for finding a p-value, and jackknife to get an estimate of contamination (Rprogram)
An example are found below:
./angsd -i my.bam -r X: -doCounts 1 -iCounts 1 -minMapQ 30 -minQ 20