Hi, I'm looking at some sequence data in order to find mutations. Since I (probably) have to filter the variants with known SNP and indels I would like to have some hint on which file format/tools you are using.
Once I have a list of candidate mutations, I planned to use BEDTools to perform most of the operations. The only problem is that I have different file formats I can operate and this puzzles me:
1- I call variants as result of samtools/samtools.pl. The format is samtools pileup
2- I have snp131 data in BED format (from UCSC genome browser)
3- I guess I can get SNPs from 1000g in VCF format (although I still have to study which is the file(s) I need).
BEDtools should support either BED and VCF format. What about samtools pileup? I guess I may try to convert it in one of both formats...
Puzzle #1 (samtools to BED):
- single nucleotide variations can be converted as CHR:POS-POS+1 (I guess)
- How do I convert small insertions? CHR:POS-POS ?
- How do I convert small deletions?
Puzzle #2 (samtools to VCF):
- Simply, is there a way to directly convert samtools pileup to VCF?
Any suggestion is appreciated :-)
Thanks
d
Once I have a list of candidate mutations, I planned to use BEDTools to perform most of the operations. The only problem is that I have different file formats I can operate and this puzzles me:
1- I call variants as result of samtools/samtools.pl. The format is samtools pileup
2- I have snp131 data in BED format (from UCSC genome browser)
3- I guess I can get SNPs from 1000g in VCF format (although I still have to study which is the file(s) I need).
BEDtools should support either BED and VCF format. What about samtools pileup? I guess I may try to convert it in one of both formats...
Puzzle #1 (samtools to BED):
- single nucleotide variations can be converted as CHR:POS-POS+1 (I guess)
- How do I convert small insertions? CHR:POS-POS ?
- How do I convert small deletions?
Puzzle #2 (samtools to VCF):
- Simply, is there a way to directly convert samtools pileup to VCF?
Any suggestion is appreciated :-)
Thanks
d
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