Loss of AD/DP info after phasing about phaser

[secastel]

Hi Mattia,
Sorry I'm a bit confused by the example line you've given.

The line "After imputing with Sanger" seems to actually be after running phASER (it includes many phASER specific tags e.g. PS:PG:PB:PI:PW:PC:PM). Can you post the example line after imputation, but before running phASER?

Stephane

[mbosio85]

Hi Stephane,
You are right, I sent the wrong line.
Here an example at each step:
Original VCF

1 534192 . C T 277.77 . AC=1;AF=0.500;AN=2;MQ=36.65; GT:AD:DP:GQ:PL 0/1:36,26:63:99:306,0,875

Here after Sanger imputation:

1 534192 rs6680723 C T . PASS TYPED;RefPanelAF=0.235818;AN=2;AC=1;INFO=1 GT:ADS:DS:GP:PS 0|1:0,1:1:0,1,0:13380

Here after phASER execution:

1 534192 rs6680723 C T . PASS TYPED;RefPanelAF=0.235818;AN=2;AC=1;INFO=1 GT:ADS:DS:GP:PS:PG:PB:PI:PW:PC:PM 0|1:0,1:1:0,1,0:13380:0/1:.:.:0|1:.:.

Are these the correct outputs I should normally get? and, if so, do you know if there is a way to keep the original information of AD and DP ?
Thanks a lot for your help

Mattia

[secastel]

Hi Mattia,
From looking at the lines you posted, it seems that the fields of interest (AD, DP) are actually removed during imputation with the Sanger Imputation Service. This is completely separate from phASER, and I have no control over how that pipeline works. phASER itself will not remove any tags that are present in the input file given to it. You could try getting in touch with someone there with your question. Sorry I couldn't be of more help.

Stephane