Dear All,
I'm working with SOLiD data. We have sequenced different strains of E.Coli with shotgun approach and our aim was to find variants (SNPs or INDELs).
I have an average coverage of 150X and I run the spectral correction on the reads to improve their quality.
I tried different softwares (Bioscope SNP calling pipeline, MAQ SNP calling pipeline and PASS). I obtain strange results:
- my bacteria seem to be diploides!!!!
- The three software give total different results. (SNPs in different positions)
Do you have any suggestion on how to approch a SNP calling with SOLiD data?
Best
Alex
I'm working with SOLiD data. We have sequenced different strains of E.Coli with shotgun approach and our aim was to find variants (SNPs or INDELs).
I have an average coverage of 150X and I run the spectral correction on the reads to improve their quality.
I tried different softwares (Bioscope SNP calling pipeline, MAQ SNP calling pipeline and PASS). I obtain strange results:
- my bacteria seem to be diploides!!!!
- The three software give total different results. (SNPs in different positions)
Do you have any suggestion on how to approch a SNP calling with SOLiD data?
Best
Alex
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