The current GATK version is 3.6-0
Examples: Monday, today, last week, Mar 26, 3/26/04

Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

Powered by Vanilla. Made with Bootstrap.
Last chance to register for the GATK workshop next week in Basel, Switzerland! http://www.sib.swiss/training/upcoming-training-events/training/gatk-workshop-lecture

ReduceRead Adding Errors.

I have a quick question about changes ReduceReads does to a file:

This is the output from a ValidateSamFile run before and after using ReduceReads on the latest nightly-build. Given that the best practices state that the SAM/BAM file must pass validation this is strange because it seems that ReduceReads is creating errors.

Any thoughts?

After:
java -jar /usr/local/picard-tools/ValidateSamFile.jar I=NA12761.mapped.ILLUMINA.bwa.CEU.exome.20121211.reduced.bam IGNORE=MISSING_TAG_NM
[Tue Nov 12 15:01:28 MST 2013] net.sf.picard.sam.ValidateSamFile INPUT=NA12761.mapped.ILLUMINA.bwa.CEU.exome.20121211.reduced.bam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Tue Nov 12 15:01:28 MST 2013] Executing as srynearson@newrepublic.genetics.utah.edu on Linux 2.6.32-358.18.1.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_25-mockbuild_2013_06_26_07_26-b00; Picard version: 1.99(1563)
ERROR: Record 20952, Read name 20524, Mate alignment does not match alignment start of mate
ERROR: Record 490879, Read name 482367, Mate alignment does not match alignment start of mate
ERROR: Record 514101, Read name 505228, Mate alignment does not match alignment start of mate
ERROR: Record 863536, Read name 849794, Mate alignment does not match alignment start of mate
ERROR: Record 1014607, Read name 998725, Mate alignment does not match alignment start of mate
ERROR: Record 1025644, Read name 1009614, Mate alignment does not match alignment start of mate
ERROR: Record 1121141, Read name 1103717, Mate alignment does not match alignment start of mate
ERROR: Record 1248134, Read name 1228854, Mate alignment does not match alignment start of mate
ERROR: Record 1278077, Read name 1258325, Mate alignment does not match alignment start of mate
ERROR: Record 1301946, Read name 1281828, Mate alignment does not match alignment start of mate

Before:
java -jar /usr/local/picard-tools/ValidateSamFile.jar I=NA12761.mapped.ILLUMINA.bwa.CEU.exome.20121211.bam IGNORE=MISSING_TAG_NM
[Tue Nov 12 15:02:01 MST 2013] net.sf.picard.sam.ValidateSamFile INPUT=NA12761.mapped.ILLUMINA.bwa.CEU.exome.20121211.bam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Tue Nov 12 15:02:01 MST 2013] Executing as srynearson@newrepublic.genetics.utah.edu on Linux 2.6.32-358.18.1.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_25-mockbuild_2013_06_26_07_26-b00; Picard version: 1.99(1563)
INFO 2013-11-12 15:03:45 SamFileValidator Validated Read 10,000,000 records. Elapsed time: 00:01:43s. Time for last 10,000,000: 103s. Last read position: 2:74,687,627

Best Answer

Answers

Sign In or Register to comment.