To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at https://software.broadinstitute.org/firecloud/documentation/freecredits

Problem with Indelrealigner assigning incorrect mate information (GATK v3.4-46-gbc02625)

kw10kw10 CambridgeMember

Mate information seems to be assigned incorrectly when the supplementary alignment is on the same chromosome as one of the non-supplementary alignments, and the primary alignments are on different chromosomes. For example:

(The first 9 columns of a SAM line for read HS36_15753:4:1106:13106:57119#25)

HS36_15753:4:1106:13106:57119#25 2209 12 2870282 60 37H38M = 2870346 0 # supplementary, second read; mate info, columns 7-9) matches the other part of the second read (with flag 161)
HS36_15753:4:1106:13106:57119#25 81 12 2870346 60 75M hs37d5 32110385 0 # first read in a pair
HS36_15753:4:1106:13106:57119#25 161 hs37d5 32110385 60 45M30S 12 2870346 0 # first part of the second read

after realignment becomes:

HS36_15753:4:1106:13106:57119#25 2209 12 2870282 60 37H38M = 2870346 139 # mate coord is correct but insert size is changed to 139
HS36_15753:4:1106:13106:57119#25 81 12 2870346 60 75M = 2870282 -139 # first read; mate info says the supplementary alignment is the mate
HS36_15753:4:1106:13106:57119#25 161 hs37d5 32110385 60 45M30S 12 2870346 0 # no change

When I run Picard FixMateInformation I get back the original alignments:

HS36_15753:4:1106:13106:57119#25 2209 12 2870282 60 37H38M = 2870346 0
HS36_15753:4:1106:13106:57119#25 81 12 2870346 60 75M hs37d5 32110385 0
HS36_15753:4:1106:13106:57119#25 161 hs37d5 32110385 60 45M30S 12 2870346 0

I noticed this problem because it causes downstream problems with duplicate marking (duplicates with the exact 3 alignments are not getting marked as duplicate)

Thanks

Tagged:

Issue · Github
by Sheila

Issue Number
71
State
closed
Last Updated
Closed By
vdauwera

Answers

Sign In or Register to comment.