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This python script parses a mpileup file to extract the coverage of each base at each position.

License: GNU General Public License v3.0

Python 100.00%
bioinformatics bioinformatics-scripts coverage mpileup parser position python27

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mpileuptools's Issues

Please specify samtools mpilleup flags to use

Thank you for creating this! Which samtools mpileup flags are expected for this tool?

It doesn't work on my pileup created from this command:
samtools mpileup -f test.fasta test.bam > pileup_test.tsv

My error:

[02/09 12:09:57] emmabishop@emmas-air:~/workspace/mpileupTools$ python2 parseMPileup.py -i ../pileup_test.tsv -p out_test
Input file is " ../pileup_test.tsv "
Output prefix file is " out_test "
Traceback (most recent call last):
  File "parseMPileup.py", line 243, in <module>
    parsePileup(inputFile, outputPrefix, separatedFiles)
  File "parseMPileup.py", line 207, in parsePileup
    lettersCount = extractCigarSeq(data[4], data[5], data[6], info);
IndexError: list index out of range

A snippet of my pileup:

[02/09 12:10:14] emmabishop@emmas-air:~/workspace/mpileupTools$ head ../pileup_test.tsv 
1	1	T	0	*	*
1	2	T	0	*	*
1	3	G	2	,,	20
1	4	A	2	,,	0/
1	5	C	3	,,,	223
1	6	C	2	,,	12
1	7	G	3	,,,	2/0
1	8	A	3	,,^?.	223
1	9	T	4	,,,.	12.3
1	10	G	2	,.	32

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