Import VCF: accept ./1 as missing call?


#1

GSK has a problem with a VCF with calls like ./1. Currently in 0.1 (and master presumably) we error. Should we accept this as missing?


#2

Would be great to have as an option for import_vcf. This change to HtsjdkRecordReader.scala allowed us to load the 25k exome pVCF generated by GLNexus:

// comment this out assert(a0.isCalled == a1.isCalled)

val gt = if (a0.isCalled && a0.isCalled == a1.isCalled) {
val i = vc.getAlleleIndex(a0)
val j = vc.getAlleleIndex(a1)
Genotype.gtIndexWithSwap(i, j)
} else null