Software for variant frequency

[sasignor]

Hello all,

I used to be able to use CLC for my SNP calling, which generates the reference base and the frequency of the variant allele in separate columns. I no longer have access to this program and have been using bwa-samtools. I have all of my files in bam format and have been generating SAM pileup tables using the -vcf option. The problem is it gives you the variant allele and consensus allele (not reference allele) and the phred scaled quality of the SNP, not its frequency. Is there a better software to use in order to get this information? Or is there a way to get this information from samtools?
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[nilshomer]

Samtools pileup gives you the reference allele, consensus call, and all bases (with strandedness) among other things.

I suggest you take a look at these pages:

http://samtools.sourceforge.net/pileup.shtml

http://samtools.sourceforge.net/cns0.shtml

[sasignor]

Ah, yes, the part about the reference allele was a typo. What I mean is I was looking for them all to be generated in separate columns - the variant, and the reference, not as part of a the read bases, as well as the frequency of the alleles as opposed to the SNP quality scores. I think something like VarScan is what I was looking for, although I am still interested as to what other people use to generate this type of output.

http://varscan.sourceforge.net/using-varscan.html

[nilshomer]

Ah, yes, the part about the reference allele was a typo. What I mean is I was looking for them all to be generated in separate columns - the variant, and the reference, not as part of a the read bases, as well as the frequency of the alleles as opposed to the SNP quality scores. I think something like VarScan is what I was looking for, although I am still interested as to what other people use to generate this type of output.

http://varscan.sourceforge.net/using-varscan.html

A few lines of code using the read bases column conditioned on the variant call and reference allele would do it. You have all the information.

[kmcarr]

Here is a script I wrote for doing this. Pass the script the name of your pileup file (created with -vcf and any other filtering) and it will output the following (as tab delimited columns):

1. Chromosome
2. Position
3. SNP (Ref > Alt base(s))
4. Consensus quality
5. Read depth
6. Alt base fraction (Alt base/Read depth)
7. Alt base %