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Created 2015-11-25 19:52:15 | Updated | Tags: varianteval interpretation

Comments (6)

I used "varianteval" module to evaluate 33 samples of mine with a ref-data across 23 chromosomes. I expected the sum of nHomVar + nHets = nSNPs but is not!!!!! I don't know why the number of "nHets" is too much large? any thoughts or clue? thanks

allSample nVariantLoci nSNPs nInsertions nDeletions nHets nHomRef nHomVar nSingletons hetHomRatio all_chr1 51144 47364 1719 2061 152157 672 33997 22615 4.48 all_chr2 37491 34738 1246 1507 102477 257 19140 18172 5.35 all_chr3 35139 32591 1163 1385 98830 386 18342 16502 5.39 all_chr4 26399 24419 864 1116 71321 198 14864 12911 4.80 all_chr5 28058 25933 958 1167 76321 290 14099 13391 5.41 all_chr6 31222 28940 1009 1273 82483 243 16410 15084 5.03 all_chr7 28351 26331 907 1113 80464 221 14682 13448 5.48 all_chr8 22551 20968 701 882 63569 224 13134 10650 4.84 all_chr9 22478 20987 679 812 60268 198 11341 11055 5.31 all_chr10 27740 25691 924 1125 79158 182 15035 12875 5.26 all_chr11 24012 22309 762 941 66762 197 14378 11521 4.64 all_chr12 25239 23310 832 1097 71793 218 15187 11800 4.73 all_chr13 12494 11547 388 559 34506 113 7156 5945 4.82 all_chr14 15825 14640 534 651 42887 123 9137 7689 4.69 all_chr15 17554 16249 585 720 49245 133 10203 8329 4.83 all_chr16 22966 21529 656 781 63713 165 13000 10825 4.90 all_chr17 23983 22285 768 930 71715 236 15978 10776 4.49 all_chr18 9741 8935 374 432 25755 93 4743 4793 5.43 all_chr19 26262 24448 792 1022 81650 359 17700 11176 4.61 all_chr20 13068 12133 431 504 37924 155 7633 6197 4.97 all_chr21 7722 7220 212 290 20928 124 4497 3807 4.65 all_chr22 14151 13188 406 557 42289 156 8814 6180 4.80 all_chr23 5330 4869 221 240 10552 92 5177 2772 2.04


Created 2013-08-20 15:43:47 | Updated | Tags: annotation interpretation variant-calling

Comments (1)

I have been trying to find documentation for understanding the annotations and numbers in the VCF file. Something like below, can someone guide me how to understand/interpret the numbers? How is the quality of the variant calling for this particular indel?

AC=2; AF=0.100; AN=20; BaseQRankSum=6.161; ClippingRankSum=-2.034; DP=313; FS=5.381; InbreedingCoeff=-0.1180; MLEAC=2; MLEAF=0.100; MQ=58.49; MQ0=0; MQRankSum=-0.456; QD=1.46; ReadPosRankSum=-4.442; VQSLOD=0.348; topculprit=ReadPosRankSum