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Why does my read-backed phasing skip a chromosome?

wesleyvanleewesleyvanlee The netherlandsMember


I am using GATK version 3.7-0 and i am performing read-backed phasing on WES data.
While running the tool I noticed it skips the variants from chr7 for some reason.
I checked the VCF and there seems nothing wrong with it. I also sorted and re-indexed the bam file but it did not solve the problem.

INFO 09:13:13,925 ProgressMeter - chr6:32648998 4.03130781E8 19.0 m 2.0 s 35.4% 53.7 m 34.7 m
INFO 09:13:43,926 ProgressMeter - chr6:32845170 4.0322476E8 19.5 m 2.0 s 35.4% 55.1 m 35.6 m
INFO 09:14:13,927 ProgressMeter - chr6:55192225 4.13146979E8 20.0 m 2.0 s 36.1% 55.4 m 35.4 m
INFO 09:14:43,928 ProgressMeter - chr6:68694284 4.16299969E8 20.5 m 2.0 s 36.5% 56.1 m 35.6 m
INFO 09:15:13,929 ProgressMeter - chr6:111700364 4.30832053E8 21.0 m 2.0 s 37.9% 55.4 m 34.4 m
INFO 09:15:43,930 ProgressMeter - chr6:151336055 4.44751474E8 21.5 m 2.0 s 39.2% 54.8 m 33.3 m
INFO 09:16:13,931 ProgressMeter - chr8:17258933 4.58947546E8 22.0 m 2.0 s 45.5% 48.3 m 26.3 m
INFO 09:16:43,932 ProgressMeter - chr8:50519118 4.71496636E8 22.5 m 2.0 s 46.6% 48.3 m 25.8 m
INFO 09:17:13,933 ProgressMeter - chr8:95709063 4.86864937E8 23.0 m 2.0 s 48.1% 47.8 m 24.8 m
INFO 09:17:43,934 ProgressMeter - chr8:139264001 5.02778661E8 23.5 m 2.0 s 49.5% 47.5 m 24.0 m
INFO 09:18:13,937 ProgressMeter - chr9:25995060 5.15352696E8 24.0 m 2.0 s 50.6% 47.5 m 23.5 m

Thanks in regards!

Wesley van Lee.

Best Answer


  • SheilaSheila Broad InstituteMember, Broadie admin

    Hi Wesley,

    The progress meter is not super accurate, so it may not be showing the chromosome in the output. Have you checked the output file to see if the skipped chromosome is indeed present?


  • wesleyvanleewesleyvanlee The netherlandsMember


    Yes i did, and they were indeed not present in the output file. The input file contains over 7.000 variants on chromosome 7. From the percentage in the output log, it looks like it did notice the variants but never phased them. Because with an average of 1% progress per .5 min from chr6 to chr8 it suddenly went up with 6.3%.

    Do you think this problem could be related to the BAM file, or is there an error in the VCF somewhere?


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