Parse samtools pileup file to get how many bases and what kind of bases are called.
Script pileup2baseindel.pl is a update version of old one pileup2base.pl. The update includes following:
- it will parse the insert and deletion too,
- it can parse pileups from multiple sample,
- you don't need to define the outputfile, instead, you will need to provide 'prefix' which will name result from each sample as prefix1.txt, prefix2.txt, etc. Default, prefix is
sample. - Provide option to define the base quality score offset, default is 33 (Sanger standard).
- Read parameters from command line with options
Pileup format is described at http://samtools.sourceforge.net/pileup.shtml. It describes information including reference allele, depth, read bases and base qualities. For read bases, we can also know the strand information for each base. However, the format is not easy for people to read. This program helps people to convert the original format into a human readable one and it can also be used as input to calcualte strand bias.
Original pileup (2 samples) input (see test.mpileup).
1 888659 T 14 c$CCCCcccCcCccc GCECEFGEEBGEE@ 11 .$...-3ATT...+2AG.+2AG.+4AGAGGG <975;:<<<<<
1 1268847 T 0 * * 11 .$.......... BGEGEEGFGEF
1 1421531 C 27 aAaaAAAAAaaaaAaAAAaAAaaAaa^]a GEDGEBGEECGCFF-DGEBGGB?FEA: C 17 .,,.,.,,,,,.,.,.. DGFEGEGBEEEGAGEGG
1 2938697 T 22 CgGGggCGgGgGGggggggggG #G=:CG#5E@E#:#A##?@C#E 20 ,,,,,..,.-4CACC.-4CACC....,.,,.^~. ==<<<<<<<<<<<::<;2<<
After apply perl pile2baseindel.pl -i test.mpileup, Here is the result.
sample1.txt
chr loc ref A T C G a t c g Insertion Deletion
1 888659 T 0 0 6 0 0 0 8 0 NA NA
1 1421531 C 13 0 0 0 14 0 0 0 NA NA
1 2938697 T 0 0 2 7 0 0 0 13 NA NA
sample2.txt (2:AG|1:AGAG means there are deletions with AG occur twice and AGAG once. NA means no insertin or deletion in this position)
chr loc ref A T C G a t c g Insertion Deletion
1 888659 T 0 9 0 2 0 0 0 0 2:AG|1:AGAG 1:ATT
1 1268847 T 0 11 0 0 0 0 0 0 NA NA
1 1421531 C 0 0 0 0 0 0 0 0 NA NA
1 2938697 T 0 11 0 0 0 9 0 0 NA 2:CACC