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 can estimate contamination, but only for chromosomes that exists in one genecopy (eg chrX for males). | 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. | ||
Angsd comes with these two files in the '''RES'''/ subfolder and these are called: | |||
An example are found below: | An example are found below: | ||
Revision as of 10:51, 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.
Angsd comes with these two files in the RES/ subfolder and these are called:
An example are found below: