Extract aligned positions from reads

Question

[María José]

Hi, I would like to know if it's possible to extract the specific positions of a target sequence that have aligned from BAM or SAM files. In this situation, more than obtaining all genomic coordinates using bedtools bamtobed. I would like to identify which positions of the reads have aligned to all genomic coordinates. For example in this picture, it would be chr3:186538693-186538967, ID1:276-550.

[Bastien Hervé]

If you are blasting your sequences you can export your results in CSV format. There you will have these metrics.

[María José]

Hi, I'm working with aligments obtained with pbmm2, minimap2 and ngmlr. I would like to obtain similar results to those generated by BLAST. I'm looking for ways to extract the target positions that have aligned.

Answer 1

[Pierre Lindenbaum]

I would like to identify which positions of the reads have aligned to all genomic coordinates.

use my tool sam2tsv : https://jvarkit.readthedocs.io/en/latest/Sam2Tsv/

https://jvarkit.readthedocs.io/en/latest/Sam2Tsv/

[María José]

Hi Pierre Lindenbaum, I’ve installed jvarkit and tested it on my data. However, I can't quite understand the output, specially regarding how to determine the genomic coordinates for the read SRR73.14 and the specific part of the sequence it has mapped to.

#Read-Name  Flag    MAPQ    CHROM   READ-POS0   READ-BASE   READ-QUAL   REF-POS1    REF-BASE    CIGAR-OP
SRR73.14    0   0   chr1    0   C   *   9999    N   S
SRR73.14    0   0   chr1    1   T   +   10000   N   S
SRR73.14    0   0   chr1    2   A   +   10001   N   S
SRR73.14    0   0   chr1    3   A   #   10002   N   M
SRR73.14    0   0   chr1    4   A   %   10003   N   M
SRR73.14    0   0   chr1    5   C   %   10004   N   M
SRR73.14    0   0   chr1    6   C   (   10005   N   M
SRR73.14    0   0   chr1    7   C   +   10006   N   M
SRR73.14    0   0   chr1    8   T   '   10007   N   M