Dears,
Recently we received data from a pilot MiSeq run: targeted human resequencing, alignments and calls generated by the on instrument software. The output files include:
Indels.1.txt
Indels.2.txt
Ma-01114-A01_S1.vcf
Ma-01114-A02_S2.vcf
SNPs.1.txt
SNPs.2.txt
Sites.1.txt
Sites.2.txt
The issue that we face is that the .vcf files are generated per sample, and therefore only call non-reference calls per sample. This makes the downstream analysis more difficult. If sample 1 is called non-reference at position X, we need to refer back to Sites.2.txt file to determine if sample 2 was called homozygous reference or was a non-call at that same position.
Before we write our own scripts to fix this, I was wondering if anyone else has already solved this problem? For example, is it possible to force the on-instrument software to include ALL calls in each of the VCF files? Alternatively, are there any utilities around that we could use to convert the Sites.txt files into VCF format?
I've done some googling and there appear to be a few abandoned threads here on SEQAnswers, but no obvious solutions so far.
Thanks!
Recently we received data from a pilot MiSeq run: targeted human resequencing, alignments and calls generated by the on instrument software. The output files include:
Indels.1.txt
Indels.2.txt
Ma-01114-A01_S1.vcf
Ma-01114-A02_S2.vcf
SNPs.1.txt
SNPs.2.txt
Sites.1.txt
Sites.2.txt
The issue that we face is that the .vcf files are generated per sample, and therefore only call non-reference calls per sample. This makes the downstream analysis more difficult. If sample 1 is called non-reference at position X, we need to refer back to Sites.2.txt file to determine if sample 2 was called homozygous reference or was a non-call at that same position.
Before we write our own scripts to fix this, I was wondering if anyone else has already solved this problem? For example, is it possible to force the on-instrument software to include ALL calls in each of the VCF files? Alternatively, are there any utilities around that we could use to convert the Sites.txt files into VCF format?
I've done some googling and there appear to be a few abandoned threads here on SEQAnswers, but no obvious solutions so far.
Thanks!