pbwt

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Bug in algorithm ReportLongMatches?

1

The algorithm 3 (`pbwt -longWithin 5`) does not report some long matches. For example, in the following example: ``` 1:1010001 001100 4:1010001 001100 0:0110000 101010 2:0011000 110010 5:0011001 000010 3:1011001...

pd3

Is it valid VCF not to 'squash' positions with more than one ALT allele?

10

I'm seeing output that looks like this: ``` 3 112841 rs78923776 C G . PASS RefPanelAF=0.000153988;AN=2;AC=0;INFO=1 GT:ADS:DS:GP 0|0:0,0:0:1,0,0 3 112841 rs78923776 C T . PASS RefPanelAF=0.078534;AN=2;AC=1;INFO=1 GT:ADS:DS:GP 0|1:0,1:1:0,1,0 ``` The...

CholoTook

Some rsIDs in original VCF not in imputed VCF

7

Looking only at chromosome 3, some 2k rsIDs (from 23andMe data) are not found in the 2.8G SNPs in imputed chromosome 3... Why should SNPs be dropped from the input...

CholoTook

Make up to date with VertebrateResequencing / pbwt ?

4

Perhaps it's my anal-retentive personality type, but the fact that you've diverged really bugs me. If you don't want to merge changes, these should be separate projects no? Cheers,

CholoTook

Please tag a stable release

2

Thanks!

sjackman

adding LICENSE file

4

It would be nice if a LICENSE file could be added. This would also make packaging it downstream easier.

bgruening

Bug in reading genotypes from VCF/BCF?

1

Hi, The code from 110 to 118 of pbwtHtslib.c in function pbwtReadVcfGT may bring a bug. ``` if (gt_arr[i] == bcf_int32_vector_end) x[i] = bcf_gt_allele(gt_arr[i-1]); // treat haploid genotypes as diploid...

dfguan

Reference impute using maximal matches: Killed

2

Hi there, I am currently trying to use PBWT to impute a reference panel A onto another reference panel B, and vice versa. I am able to impute reference panel...

jerrywzy

At some point between commit 9a1e0fe and c9764e2, there seems to have been a bug introduced to the writePhase code. The phase file output is now writing raw binary 0/1...

grady