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williamslab / ped-sim

Pedigree simulator
GNU General Public License v3.0
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Update documentation for the input VCF to require only GT in the FORMAT field #5

Closed nh13 closed 5 years ago

nh13 commented 5 years ago

I have found that the format fields for all individuals must only contain the GT tag. If I specify any other tag, some of the genotypes get very odd formats. See the second sample in this example.

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  trio1_g2-b1-i1  trio1_g2-b2-i1
chr1    752721  rs3131972   A   G   .   PASS    .   GT:PS   0|1:752721  0:752721|0
chr1    838555  rs4970383   C   A   .   PASS    .   GT:PS   1|0:752721  0:752721|0
chr1    846808  rs4475691   C   T   .   PASS    .   GT:PS   0|0:752721  1:752721|0
chr1    854250  rs7537756   A   G   .   PASS    .   GT:PS   0|0:752721  1:752721|0
chr1    861808  rs13302982  A   G   .   PASS    .   GT:PS   0|1:752721  0:752721|1
chr1    888659  rs3748597   T   C   .   PASS    .   GT:PS   1|1:752721  1:752721|0
chr1    894573  rs13303010  G   A   .   PASS    .   GT:PS   0|0:752721  0:752721|1
chr1    897564  rs13303229  T   C   .   PASS    .   GT:PS   1|1:752721  1:752721|0
chr1    918573  rs2341354   A   G   .   PASS    .   GT:PS   0|0:752721  0:752721|0
chr1    990417  rs2465136   T   C   .   PASS    .   GT:PS   0|1:752721  1:752721|1
chr1    998395  rs7526076   A   G   .   PASS    .   GT:PS   1|1:752721  1:752721|0
chr1    1018704 rs9442372   A   G   .   PASS    .   GT:PS   1|0:752721  0:752721|0
chr1    1040026 rs6671356   T   C   .   PASS    .   GT:PS   0|0:752721  1:752721|1
chr1    1062638 rs9442373   C   A   .   PASS    .   GT:PS   0|0:752721  0:752721|0
chr1    1097335 rs9442385   T   G   .   PASS    .   GT:PS   1|1:752721  1:752721|0
chr1    1110019 rs11260542  A   G   .   PASS    .   GT:PS   0|0:752721  0:752721|0
chr1    1113121 rs12092254  G   A   .   PASS    .   GT:PS   0|0:752721  0:752721|0
chr1    1130727 rs10907175  A   C   .   PASS    .   GT:PS   0|0:752721  0:752721|0
chr1    1158277 rs3813199   G   A   .   PASS    .   GT:PS   0|0:752721  0|0
chr1    1178925 rs12093154  G   A   .   PASS    .   GT:PS   0|0:752721  0|0
chr1    1203938 rs4018608   T   C   .   PASS    .   GT:PS   0|0:752721  0|1
chr1    1220136 rs2144440   A   G   .   PASS    .   GT:PS   0|1:752721  0|0
chr1    1227897 rs3737721   A   G   .   PASS    .   GT:PS   0|0:752721  0|1
chr1    1258246 rs3845293   A   C   .   PASS    .   GT:PS   0|0:752721  0|1
chr1    1305561 rs17160669  C   T   .   PASS    .   GT:PS   0|1:752721  0|0
chr1    1335302 rs1240707   C   T   .   PASS    .   GT:PS   0|0:752721  0|0
williamslab commented 5 years ago

Thank you. I've added this to the documentation.