Hi! I am doing indel analysis, using SAMtools/bcftools. First I tried to use mpileup with the command line:
samtools mpileup file.fa file.bam | bcftools view -bvcg - > var.raw.bcf
bcftools view var.raw.bcf | vcfutils.pl varFilter -D100 > var.flt.vcf
I tried also the options at different time: –C50, -D8000, –d8000, -A, –BQ0, –r Chr and -r Chr:1-100 (interval in a chromosome).
I had results for small parts of a chromosome. I had for a entire chromosome only when it is very small chromosome. Each time, the analysis stopped in a different region of the chromosome. So, for example for a big chromosome, I ran the analysis more than 10 times and I was not able to get for all chromosome (changing the regions using -r Chr:1-100; -r Chr:100-200, etc).
After we tried the analysis with pileup (other version of SAMtools), and the analysis was ok, for the same files.
Please, what do you think could be the problem? Should we use the mpileup instead of pileup? Why? I don’t want to do for each chromosome separately; I only tried this option to understand the problem.
Thanks
Clarissa
samtools mpileup file.fa file.bam | bcftools view -bvcg - > var.raw.bcf
bcftools view var.raw.bcf | vcfutils.pl varFilter -D100 > var.flt.vcf
I tried also the options at different time: –C50, -D8000, –d8000, -A, –BQ0, –r Chr and -r Chr:1-100 (interval in a chromosome).
I had results for small parts of a chromosome. I had for a entire chromosome only when it is very small chromosome. Each time, the analysis stopped in a different region of the chromosome. So, for example for a big chromosome, I ran the analysis more than 10 times and I was not able to get for all chromosome (changing the regions using -r Chr:1-100; -r Chr:100-200, etc).
After we tried the analysis with pileup (other version of SAMtools), and the analysis was ok, for the same files.
Please, what do you think could be the problem? Should we use the mpileup instead of pileup? Why? I don’t want to do for each chromosome separately; I only tried this option to understand the problem.
Thanks
Clarissa
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