Hello,
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.