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Rs values missing from pileupCaller output #4

Closed teepean closed 4 years ago

teepean commented 5 years ago

Hello!

I was wondering if there is a way to keep the rs values when creating Eigenstrat files with pileupCaller? At the moment the output looks like this. I am using HumanOriginsPublic2068.snp as the Eigenstrat positions file.

1_752566 1 0 752566 G A 1_842013 1 0 842013 T G 1_891021 1 0 891021 G A 1_903426 1 0 903426 C T 1_949654 1 0 949654 A G 1_1018704 1 0 1018704 A G 1_1045331 1 0 1045331 G A 1_1048955 1 0 1048955 A G 1_1061166 1 0 1061166 T C 1_1108637 1 0 1108637 G A 1_1120431 1 0 1120431 G A 1_1156131 1 0 1156131 T C 1_1157547 1 0 1157547 T C 1_1158277 1 0 1158277 G A 1_1161780 1 0 1161780 C T 1_1170587 1 0 1170587 C T 1_1205155 1 0 1205155 A C

stschiff commented 5 years ago

Yes, that was a choice that makes sense in our internal processing pipeline, but indeed isn’t a good default. I will change that and will let you know when it’s done.

Stephan

On 9 Feb 2019, at 19:23, teepean notifications@github.com wrote:

Hello!

I was wondering if there is a way to keep the rs values when creating Eigenstrat files with pileupCaller? At the moment the output looks like this. I am using HumanOriginsPublic2068.snp as the Eigenstrat positions file.

1_752566 1 0 752566 G A 1_842013 1 0 842013 T G 1_891021 1 0 891021 G A 1_903426 1 0 903426 C T 1_949654 1 0 949654 A G 1_1018704 1 0 1018704 A G 1_1045331 1 0 1045331 G A 1_1048955 1 0 1048955 A G 1_1061166 1 0 1061166 T C 1_1108637 1 0 1108637 G A 1_1120431 1 0 1120431 G A 1_1156131 1 0 1156131 T C 1_1157547 1 0 1157547 T C 1_1158277 1 0 1158277 G A 1_1161780 1 0 1161780 C T 1_1170587 1 0 1170587 C T 1_1205155 1 0 1205155 A C

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teepean commented 5 years ago

Yes, that was a choice that makes sense in our internal processing pipeline, but indeed isn’t a good default. I will change that and will let you know when it’s done. Stephan

Thank you!

teepean commented 4 years ago

Looks like this was fixed recently.

stschiff commented 4 years ago

Yes, sorry. Indeed, never clarified this was fixed indeed.