#1 Please consider adding header and sample fields in vcf files

[Miika Ahdesmaki]

It would be super nice if Scalpel produced the INFO, FILTER and FORMAT fields in the header of vcf output, see http://www.1000genomes.org/node/101. This would add better compatibility with the Gatk tools.

It would also be great if the sample fields were populated, providing the GT, DP and maybe other tags.

[Giuseppe Narzisi]

done!

[Miika Ahdesmaki]

Thanks! In looking at the code and running some examples, I noticed that "$altcov" points to reference allele depth and "$mincov" to the alternative allele depth. I wonder if I'm missing something? Thus my proposition to use my $format_val = "$gt:$altcov,$mincov:$totcov"; (instead of my $format_val = "$gt:$mincov,$altcov:$totcov";)

[Giuseppe Narzisi]

$mincov is the minimum coverage of the specific mutation described in the vcf line
$altcov is the total coverage of any other allele (reference + other mutations)

[Miika Ahdesmaki]

Makes sense now!

[Miika Ahdesmaki]

Further, it would be nice if after FORMAT there'd a the sample name, picked e.g. from the @RG SM field. For example, for the below @RG the sample name would be 10-497-T:
@RG ID:2 PL:illumina PU:2_2014-02-18_tumor-paired SM:10-497-T