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.
SnpFilters: Difference between revisions
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Angsd has different snpfilters. | Angsd has different snpfilters/snpstats. | ||
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These statistics will be calculated and reported and written into a file called '''PREFIX.snpStat.gz''' | These statistics will be calculated and reported and written into a file called '''PREFIX.snpStat.gz''' | ||
The HWE requies -dohwe which is depended on domaf. So a full example would be: | |||
<pre> | |||
./angsd -b list -domaf 1 -domajorminor 1 -gl 1 -snp_pval 1e-2 -hwe_pval 1 -P 5 -dosnpstat 1 | |||
</pre> | |||
Please notice that '''-doSnpStat 1''' does not filter out sites, but will only report stats. In the above command we therefore limit the analysis and output to the sites that are likely to be truly variable (-snp_pval 1e-2). But we calculate HWE deviations from all sites, but does not filter by it (-hwe_pval 1) | |||
Revision as of 17:20, 27 March 2015
Angsd has different snpfilters/snpstats.
- SB1 strand bias1
- SB2 strand bias2
- SB3 strand bias3
- deviation from HWE
- Wilcox rank sum test for position in read
The 3 strand bias filters are described here: http://www.biomedcentral.com/1471-2164/13/666
The deviation from HWE is described in http://www.ncbi.nlm.nih.gov/pubmed/23950147
The wilcox rank sum test is not described anywhere
These statistics will be calculated and reported and written into a file called PREFIX.snpStat.gz
The HWE requies -dohwe which is depended on domaf. So a full example would be:
./angsd -b list -domaf 1 -domajorminor 1 -gl 1 -snp_pval 1e-2 -hwe_pval 1 -P 5 -dosnpstat 1
Please notice that -doSnpStat 1 does not filter out sites, but will only report stats. In the above command we therefore limit the analysis and output to the sites that are likely to be truly variable (-snp_pval 1e-2). But we calculate HWE deviations from all sites, but does not filter by it (-hwe_pval 1)