Dear All
I am trying to identify snps using GATK tool. Their manual suggested that I shall try to validate my bam files before entering the analytic pipeline.
My samples are 100 nucleotides long (first 3 sites trimmed) paired reads.
I generated bam files for each sample using tophat 1.33 and I sorted each bam file (one file per sample) using picard ReorderSam.jar,
After that I added read group information using Picard AddOrReplaceReadGroups.jar.
Then I ran a ValidateSamFile.jar to check whether these bam files are suitable in GATK pipeline. However, I got a lot of errors like this.
Can anyone tell me where the problem is? Why do I have so many unmatched pairs identified at this step. Should I delete them before the analysis?
Thanks a lot.
I am trying to identify snps using GATK tool. Their manual suggested that I shall try to validate my bam files before entering the analytic pipeline.
My samples are 100 nucleotides long (first 3 sites trimmed) paired reads.
I generated bam files for each sample using tophat 1.33 and I sorted each bam file (one file per sample) using picard ReorderSam.jar,
After that I added read group information using Picard AddOrReplaceReadGroups.jar.
Then I ran a ValidateSamFile.jar to check whether these bam files are suitable in GATK pipeline. However, I got a lot of errors like this.
ERROR: Record 21368, Read name HWI-ST978:1370AHMACXX:5:1308:13890:200017, Mate alignment does not match alignment start of mate
ERROR: Record 21368, Read name HWI-ST978:1370AHMACXX:5:1308:13890:200017, Mate negative strand flag does not match read negative strand flag of mate
ERROR: Record 21377, Read name HWI-ST978:1370AHMACXX:5:1308:13890:200017, Mate alignment does not match alignment start of mate
ERROR: Record 21377, Read name HWI-ST978:1370AHMACXX:5:1308:13890:200017, Mate negative strand flag does not match read negative strand flag of mate
ERROR: Record 21477, Read name HWI-ST978:1370AHMACXX:5:1306:2629:199972, Mate alignment does not match alignment start of mate
ERROR: Record 21477, Read name HWI-ST978:1370AHMACXX:5:1306:2629:199972, Mate negative strand flag does not match read negative strand flag of mate
ERROR: Record 21481, Read name HWI-ST978:1370AHMACXX:5:1306:2629:199972, Mate alignment does not match alignment start of mate
ERROR: Record 21481, Read name HWI-ST978:1370AHMACXX:5:1306:2629:199972, Mate reference index (MRNM) does not match reference index of mate
ERROR: Record 21490, Read name HWI-ST978:1370AHMACXX:5:2108:3190:30134, Mate alignment does not match alignment start of mate
ERROR: Record 21490, Read name HWI-ST978:1370AHMACXX:5:2108:3190:30134, Mate negative strand flag does not match read negative strand flag of mate
ERROR: Record 21368, Read name HWI-ST978:1370AHMACXX:5:1308:13890:200017, Mate negative strand flag does not match read negative strand flag of mate
ERROR: Record 21377, Read name HWI-ST978:1370AHMACXX:5:1308:13890:200017, Mate alignment does not match alignment start of mate
ERROR: Record 21377, Read name HWI-ST978:1370AHMACXX:5:1308:13890:200017, Mate negative strand flag does not match read negative strand flag of mate
ERROR: Record 21477, Read name HWI-ST978:1370AHMACXX:5:1306:2629:199972, Mate alignment does not match alignment start of mate
ERROR: Record 21477, Read name HWI-ST978:1370AHMACXX:5:1306:2629:199972, Mate negative strand flag does not match read negative strand flag of mate
ERROR: Record 21481, Read name HWI-ST978:1370AHMACXX:5:1306:2629:199972, Mate alignment does not match alignment start of mate
ERROR: Record 21481, Read name HWI-ST978:1370AHMACXX:5:1306:2629:199972, Mate reference index (MRNM) does not match reference index of mate
ERROR: Record 21490, Read name HWI-ST978:1370AHMACXX:5:2108:3190:30134, Mate alignment does not match alignment start of mate
ERROR: Record 21490, Read name HWI-ST978:1370AHMACXX:5:2108:3190:30134, Mate negative strand flag does not match read negative strand flag of mate
Thanks a lot.
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