Going From Cigar String In Sam To Genomic Coordinates?

Question

[User 9996]

How can I go from a CIGAR string, given in the SAM output format, to a set of start/end genomic coordinates for paired-end sequences? The SAM format gives the start coordinate but I need to find the end coordinate as well. Thanks.

Answer 1

[Pierre Lindenbaum]

Have a look at the Cigar.java source code in Picard. For example:

/**
 * @return The number of reference bases that the read covers, including padding.
 */
public int getPaddedReferenceLength() {
    int length = 0;
    for (final CigarElement element : cigarElements) {
        switch (element.getOperator()) {
            case M:
            case D:
            case N:
            case EQ:
            case X:
            case P:
                length += element.getLength();
        }
    }
    return length;
}

[Jonathan Manning]

Once you have length, the position of the last base is: end = start + length - 1. Don't forget the minus one, since we're "counting fenceposts" (google it).

Answer 2

[Aaronquinlan]

The bamToBed program in BEDTools will do this by create BED entries for each BAM alignment where the end end coordinate reflects the CIGAR string. Moreover, if you want to create separate BED entries for "spliced" or "split" alignments (i.e., when there is an "N: CIGAR op present), use the -split option.

[Jonathan Manning]

Just remember, BED entries are 0-indexed, half-open ranges (up to but not including the end position). A 5 bp read starting at (1-based) position 10 would be "chr1 9 15" in BED.

[Varun Gupta]

Hi

I am trying the split option on my bam file and it is only reporting 6 fields in the output and that too for all the alignments. Can you suggest what is going wrong??