scottrk
commented
8 years ago Hmmm...interesting. There are going to be some big patches landing soon. Maybe those will fix this issue. I'll let you know when those land so you can test that out.
On 5/5/16 9:35 AM, noellenoyes wrote:
Every time I run Consensus_Maker.py script, it drops exactly 1 read from the sorted bam file. When I went back to trace down this error using the tagcounts file and the corresponding sam file, I found that it always misses the first read in the (sorted) sam file (so, the first read in the corresponding sorted bam file as well). I am not a strong python coder, so not sure where/why this is occurring, but I'm nearly positive it isn't my use of samtools view or sort in the intervening steps between bwa sampe and Consensus_Maker.py.
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Every time I run Consensus_Maker.py script, it drops exactly 1 read from the sorted bam file. When I went back to trace down this error using the tagcounts file and the corresponding sam file, I found that it always misses the first read in the (sorted) sam file (so, the first read in the corresponding sorted bam file as well). I am not a strong python coder, so not sure where/why this is occurring, but I'm nearly positive it isn't my use of samtools view or sort in the intervening steps between bwa sampe and Consensus_Maker.py.