ignore the `FILTER` field in the vcf file?

zkutalik / ssimp_software

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ignore the `FILTER` field in the vcf file? #94

Closed aaronmcdaid closed 6 years ago

aaronmcdaid commented 6 years ago

The current version of ssimp (up to and including 0.5.3) uses the DISCARD_FILTERED the libStatGen which results in some rows being discarded. The effect of this is that ssimp fails with some reference panels.

In this PR, I remove this check.

But, should we proceed with this change? The question is: do we care about the FILTER field in the vcf. Typical values are . and PASS. Should be ignore that field? Should we require FILTER=PASS?

aaronmcdaid commented 6 years ago

As discussed in the other thread, we will just ignore the FILTER field. I have therefore merged this code and called it v0.5.4

sinarueeger commented 6 years ago

made a PR with the osx binary in #96 .