Comments (2)
Hello! Thank you for your interest in my software! My apologies for the delay in replying I'm currently on paternity leave.
This is not really a bug, it is more like a feature. I did not expect that it caller would simultaneously produce PL and GL. It does not make much sense. If I had more time I could add a flag to accept such format. However, I have very little time during the day.
Could you try to modify the input file to remove the pl field?
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Thanks for your reply! I used bcftools to remove the PL field. And after I did so, the glactools began to work successfully. I'll put my code here to help others who may encounter the similar problems. And you can close this issue. Thanks one more time.
bcftools view --header-only chr22.vcf.gz >> chr22.vcf
bcftools query -f '%CHROM\t%POS\t%ID\t%REF\t%ALT\t%QUAL\t%FILTER\t%INFO\tGT:GQ:DP:AD:VAF:GL[\t%GT:%GQ:%DP:%AD:%VAF:%GL]\n' chr22.vcf.gz >> chr22.vcf
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Related Issues (20)
- cannot determine the root allele
- install error HOT 1
- compile errors HOT 4
- run error about Cannot write to /dev/stdout. HOT 16
- Can not use bed track with glactools bam2acf HOT 1
- SQ fields differ in the header HOT 1
- plink(bed-bim-fam) to treemix HOT 5
- vcf to G-phocs HOT 1
- bam2acf for multiple samples HOT 1
- vcf to GROSS convertion HOT 2
- install issue HOT 2
- epo file format HOT 27
- vcfm2acf issue HOT 17
- installation trouble HOT 4
- --onlyGT confusion HOT 1
- Error in vcfm2acf HOT 9
- vcfm2acf deal for vcf file HOT 15
- issue with setting root HOT 5
- compilation terminated, make[1]: *** [Makefile:139: bam_tview_curses.o] Error 1 & make: *** [Makefile:44: samtools/libst.a] Error 2 HOT 1
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