Parsing snpeff vcf to maff error

[MiguelJulia]

Hi,

I am trying to parse a vcf created by snpeff to get a maf file, but I get the following error:

[miguel]$ python /bmm/home/mj308/vcf2maf-master/vcf2maf/vcf2maf.py -v --maf par.realigned.bam.filtered.vcf.snpeff.maf par.realigned.bam.filtered.vcf.snpeff.vcf
processing file: par.realigned.bam.filtered.vcf.snpeff.vcf
Traceback (most recent call last):
File "/bmm/home/mj308/vcf2maf-master/vcf2maf/vcf2maf.py", line 556, in
main()
File "/bmm/home/mj308/vcf2maf-master/vcf2maf/vcf2maf.py", line 543, in main
n += vcf2maf(vcf_file, maf_file, decrement_end_coordinate=args.decrement_end_coordinate, verbose=args.verbose)
File "/bmm/home/mj308/vcf2maf-master/vcf2maf/vcf2maf.py", line 182, in vcf2maf
vcf_reader = vcf.Reader(vcf_file)
File "/usr/lib/python2.6/site-packages/PyVCF-0.6.8.dev0-py2.6.egg/vcf/parser.py", line 296, in init
self._parse_metainfo()
File "/usr/lib/python2.6/site-packages/PyVCF-0.6.8.dev0-py2.6.egg/vcf/parser.py", line 322, in _parse_metainfo
key, val = parser.read_filter(line)
File "/usr/lib/python2.6/site-packages/PyVCF-0.6.8.dev0-py2.6.egg/vcf/parser.py", line 143, in read_filter
"One of the FILTER lines is malformed: %s" % filter_string)
SyntaxError: One of the FILTER lines is malformed: ##FILTER=<ID=LOWQUAL,Description="Set if not true: (%TYPE="snp" && %QUAL>=30) || (%TYPE="indel" && %QUAL>=60)">

How can I solve it?

Thanks,

Miguel

[cbare]

Hi Miguel,

Sorry, I didn't see this for quite a while. I'm no longer maintaining this code. Perhaps, have a look at mskcc's vcf2maf?