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picard tools FilterSamReads

jainyjainy salt lake cityMember

Hi
I am trying to extract reads from a Read list file from a bam file using the command using FilterSamReads option. At first I got the "SAM validation error: ERROR: Record 174124896, Read name ERR233302.68152322, MAPQ should be 0 for unmapped read.". Then I tried with
the VALIDATION_STRINGENCY=LENIENT option. It works fine without getting killed but I am not getting the read pair that is mapped else where or (unmapped). Please let me know how can I get around this.

picard.sam.FilterSamReads INPUT=NA12234.mapped.ILLUMINA.bwa.CEU.low_coverage.20130415.bam FILTER=includeReadList [OUTPUT SAM/BAM will contain reads that are supplied in the READ_LIST_FILE file] READ_LIST_FILE=NA122349:33130-33138.allpairedendreadIDs.txt OUTPUT=NA122349:33130314-33130814.allpairedendread.bam VALIDATION_STRINGENCY=LENIENT WRITE_READS_FILES=true VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Mon Apr 10 16:41:43 MDT 2017] Executing as [email protected] on Linux 2.6.32-642.13.1.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_121-b13; Picard version: 2.8.1-SNAPSHOT
Ignoring SAM validation error: ERROR: Record 174124896, Read name ERR233302.68152322, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 209073874, Read name ERR233302.12055857, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 209073875, Read name ERR233302.87427881, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 209073876, Read name ERR233302.91489012, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 209073877, Read name ERR233302.91942085, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 209073878, Read name ERR233302.100387733, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 209073879, Read name ERR233302.12935339, MAPQ should be 0 for unmapped read.

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