ANGSD: Analysis of next generation Sequencing Data
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SnpFilters: Difference between revisions
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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) | 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) | ||
=Example Output= | |||
<pre> | |||
hromo Position +Major +Minor -Major -Minor SB1:SB2:SB3 HWE_LRT:HWE_pval baseQ_Z:baseQ_pval | |||
1 14000023 45 0 22 4 -2.730769:0.163031:0.015386 0.060143:8.062706e-01 -1.882799:5.972750e-02 | |||
1 14000072 58 0 43 1 -2.318182:0.022952:0.431373 -0.000006:1.000000e+00 -1.647226:9.951167e-02 | |||
1 14000202 33 0 24 15 -1.846154:0.485830:0.000023 -0.000021:1.000000e+00 -2.114540:3.446902e-02 | |||
1 14000873 41 20 56 21 0.185598:0.339238:0.574272 1.973686:1.600571e-01 -3.496682:4.711723e-04 | |||
1 14001018 37 14 32 11 0.070296:0.278303:1.000000 1.759127:1.847334e-01 -3.037824:2.383068e-03 | |||
1 14001501 80 1 66 1 -0.190897:0.014943:1.000000 -0.000002:1.000000e+00 -0.357063:7.210450e-01 | |||
1 14001867 46 21 52 13 0.440386:0.337740:0.165207 0.288166:5.913983e-01 -1.961795:4.978620e-02 | |||
1 14002342 52 1 53 3 -0.945670:0.054563:0.618547 0.659996:4.165614e-01 -0.161165:8.719638e-01 | |||
1 14002422 41 17 29 20 -0.332741:0.441037:0.228091 6.478374:1.091948e-02 -0.822001:4.110760e-01 | |||
1 14002474 66 6 46 5 -0.164439:0.098696:0.761125 -0.000012:1.000000e+00 -1.763711:7.778050e-02 | |||
1 14002970 47 0 50 4 -1.870370:0.077129:0.121143 -0.000094:1.000000e+00 -2.411706:1.587805e-02 | |||
1 14003581 59 22 53 18 0.068718:0.275157:0.854787 0.870476:3.508235e-01 -1.033482:3.013785e-01 | |||
1 14004473 57 2 59 1 0.683522:0.034195:0.618617 -0.000022:1.000000e+00 -1.067950:2.855431e-01 | |||
1 14004623 57 21 56 34 -0.331562:0.410438:0.142272 0.616781:4.322460e-01 -1.788061:7.376604e-02 | |||
1 14005069 73 4 77 1 1.212954:0.052991:0.209619 -0.000002:1.000000e+00 -1.002612:3.160481e-01 | |||
</pre> | |||
Revision as of 16:21, 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)
Example Output
hromo Position +Major +Minor -Major -Minor SB1:SB2:SB3 HWE_LRT:HWE_pval baseQ_Z:baseQ_pval 1 14000023 45 0 22 4 -2.730769:0.163031:0.015386 0.060143:8.062706e-01 -1.882799:5.972750e-02 1 14000072 58 0 43 1 -2.318182:0.022952:0.431373 -0.000006:1.000000e+00 -1.647226:9.951167e-02 1 14000202 33 0 24 15 -1.846154:0.485830:0.000023 -0.000021:1.000000e+00 -2.114540:3.446902e-02 1 14000873 41 20 56 21 0.185598:0.339238:0.574272 1.973686:1.600571e-01 -3.496682:4.711723e-04 1 14001018 37 14 32 11 0.070296:0.278303:1.000000 1.759127:1.847334e-01 -3.037824:2.383068e-03 1 14001501 80 1 66 1 -0.190897:0.014943:1.000000 -0.000002:1.000000e+00 -0.357063:7.210450e-01 1 14001867 46 21 52 13 0.440386:0.337740:0.165207 0.288166:5.913983e-01 -1.961795:4.978620e-02 1 14002342 52 1 53 3 -0.945670:0.054563:0.618547 0.659996:4.165614e-01 -0.161165:8.719638e-01 1 14002422 41 17 29 20 -0.332741:0.441037:0.228091 6.478374:1.091948e-02 -0.822001:4.110760e-01 1 14002474 66 6 46 5 -0.164439:0.098696:0.761125 -0.000012:1.000000e+00 -1.763711:7.778050e-02 1 14002970 47 0 50 4 -1.870370:0.077129:0.121143 -0.000094:1.000000e+00 -2.411706:1.587805e-02 1 14003581 59 22 53 18 0.068718:0.275157:0.854787 0.870476:3.508235e-01 -1.033482:3.013785e-01 1 14004473 57 2 59 1 0.683522:0.034195:0.618617 -0.000022:1.000000e+00 -1.067950:2.855431e-01 1 14004623 57 21 56 34 -0.331562:0.410438:0.142272 0.616781:4.322460e-01 -1.788061:7.376604e-02 1 14005069 73 4 77 1 1.212954:0.052991:0.209619 -0.000002:1.000000e+00 -1.002612:3.160481e-01