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alachins / raisd

RAiSD: software to detect positive selection based on multiple signatures of a selective sweep and SNP vectors
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start position and end position is 0 when adding -R parameter #19

Open weikai-320722 opened 4 years ago

weikai-320722 commented 4 years ago

hello!

when I add -R, I got a report that all start and end position is 0, like this: ../RAiSD -n chr01 -I Spenn-ch01.biallelic.recode.vcf -R -G 1093 // Spenn-ch01 105398 0 0 7.033e+00 7.732e-02 4.648e-01 2.147e-01 205494 0 0 7.074e-01 3.441e-01 1.146e+00 2.791e-01 305591 0 0 5.672e-01 3.961e-01 1.252e+00 2.812e-01 405687 0 0 4.414e-01 2.829e-01 2.012e+00 2.512e-01 505784 0 0 2.972e+00 4.526e-01 1.361e+00 1.831e+00 605881 0 0 6.415e-01 4.526e-01 1.655e+00 4.804e-01 705977 0 0 3.150e+00 4.526e-01 1.500e+00 2.136e+00 806074 0 0 9.926e-01 5.658e-01 1.813e+00 1.027e+00 906170 0 0 8.267e-01 1.862e+00 2.178e+00 3.353e+00 1006267 0 0 1.887e+00 1.697e-01 4.368e-01 1.400e-01 1106363 0 0 1.988e+00 2.829e-01 4.779e-01 2.810e-01 1206460 0 0 3.738e-01 6.564e-01 9.352e-01 2.300e-01 1306557 0 0 2.727e-01 1.539e+00 1.251e+00 5.247e-01 1406653 0 0 6.665e-01 6.430e-01 1.150e+00 4.919e-01 1506750 0 0 7.652e-01 1.132e-01 1.364e+00 1.182e-01 1606846 0 0 5.100e-01 1.072e+00 1.394e+00 7.629e-01 1706943 0 0 2.092e+00 6.750e-01 1.076e+00 1.519e+00

alachins commented 4 years ago

The tool does not report start/stop positions when -G is used. You can get the start/stop positions for all evaluated locations if you omit the -G parameter.

weikai-320722 commented 4 years ago

Thanks for your quick response! I also performed SweeD to detect CLR. But when I use same -gird parameter to run RAiSD with SweeD, I can't get same position to calculate value.

SweeD command line: ../SweeD -name chr01 -input Spenn-ch01.biallelic.recode.vcf -grid 1093

RAiSD command line: ../RAiSD -n chr01 -I Spenn-ch01.biallelic.recode.vcf -CO SweeD_chr01_Report 1 2 -G 1093 -c 2 -COT 0.05 -O -COD 400

alachins commented 4 years ago

The maths to compute the positions to report scores slightly differ in SweeD and RAiSD. This is why -COD is there. It relaxes the requirement for exact positions. You can try -COD 2 to check if there are any exact matches.