question regarding input vcf about phaser

[secastel]

Hi Laur,

You can absolutely use an unphased VCF as input. It will just reduce the maximum length (and number of variants) that can be summed across when generating the counts. The phaser gene AE script will automatically select the phased haplotype with the greatest read depth and use that to generate the counts.

• Stephane

[lyj95618]

Thanks for answering my question!

Just two more things:

1. when WGS/WES is unavailable, is it possible to use panel sequence VCF file as the input VCF? will it work if I am only interested in a particular gene?

2. Would you recommend to perform "remove duplicated read (e.g. Picard)" before inputting the bam to phaser?

Thanks,
Laur

[secastel]

If by panel you mean genotyping array, then yes it should work. Theoretically it will work with any genotyping platform, provided of course that the genotype calls are accurate.

As for duplicate reads, I'd suggest reading our 2015 paper, where we discussing duplicate reads (https://link.springer.com/article/10.1186/s13059-015-0762-6)

[lyj95618]

Thank you very much for the reply!