Thanks for the code citation!
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Alex Reynolds
What is this result from samtools idxstats?
When running samtools idxstats on an indexed BAM file foo.bam in order to build a list of chromosomes, I get a result that includes a line I'm not sure how to interpret:
$ samtools idxstats foo.bam | cut -f1
chr1
chr10
chr11
...
chrY
*
What is the asterisk supposed to refer to, when I iterate through this list and extract data from that chromosome?
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Ram
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Alex Reynolds
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Alex Reynolds
1 answer
in the code of bam_index.c
printf("*\t0\t0\t%llu\n", (long long)idx->n_no_coor);
where n_no_coor = "unmapped reads without coordinate"
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Pierre Lindenbaum
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Pierre Lindenbaum
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Thanks :-) Lige hvad jeg skulle bruge.