Dear all,
I am new to the new gen seq and have a bit of a problem using PICARD.
Basically, I have Illumina paired-end sequencing that was aligned with BWA and converted to sorted and indexed bam file with samtools. I am trying to collect some summary statistics on the number of mapped and unmapped reads, by using the CollectAlignmentSummaryMetrics in PICARD. PICARD reports the correct number of reads, but 0 for any of the metrics for aligned reads, i.e. all reads are unmapped.
By looking at the sam file, I could see that a lot of the reads are mapped, e.g. bitwise flags of 147 and 99 for the pairs or 0x1+0x2+0x10+0x80 and 0x1+0x2+0x20+0x40, therefore no problems as far as I can see.
Just cannot understand why PICARD reports that all reads are unmapped. Any help would be much appreciated.
I am new to the new gen seq and have a bit of a problem using PICARD.
Basically, I have Illumina paired-end sequencing that was aligned with BWA and converted to sorted and indexed bam file with samtools. I am trying to collect some summary statistics on the number of mapped and unmapped reads, by using the CollectAlignmentSummaryMetrics in PICARD. PICARD reports the correct number of reads, but 0 for any of the metrics for aligned reads, i.e. all reads are unmapped.
By looking at the sam file, I could see that a lot of the reads are mapped, e.g. bitwise flags of 147 and 99 for the pairs or 0x1+0x2+0x10+0x80 and 0x1+0x2+0x20+0x40, therefore no problems as far as I can see.
Just cannot understand why PICARD reports that all reads are unmapped. Any help would be much appreciated.
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