rcheng
rcheng
The following GT:PL:DP:AD:GP:GQ are observed in a male on chrX 1:230,235:38:22,16:-nan:127 0:20,38:5:3,2:0.940634,0.0593659:12 0:35,64:13:9,4:0.99192,0.00808017:20 Notes: 1) PL is not normalized; 2) Both REF and ALT alleles exist, e.g. AD = 22,16;...
The vcf file was generated by bcftools call
By the way, bcftools call -S worked well using a samples-file. Unfortunately, bcftools convert -S and bctfools view -S failed if the same samples-file was supplied. For instance, bcftools view...
Code (testBcftools.s) and data are available at https://palmerlab.s3.sdsc.edu/minio/debug/. Both "-nan" and the "bcftools call -S" error can be reproduced.