Harriet Dashnow

Output VCF

3

Use this: https://github.com/mflevine/hts-nim-sugar

Inconsistent soft-clipped reads are ignored when calculating bounds, see #90 However, they do still contribute to center mass and to allele length calculations. Keeping this here as a reminder in...

> Hi Harriet—another suggestion would be to support hemizygous calls in males on chrX. This is important for Fragile X and Kennedy disease (SBMA) in particular. You’d have to pass...

Evaluate bounds soft-clip support using entropy

1

Use entropy to distinguish defined from dispersed soft-clips supporting bounds.

Hide these parameters to discourage users from changing them without careful consideration ``` --proportion-repeat --min-mapq --min-support --min-clip --min-clip-total ```

`strling.nimble` and `src/strpkg/version.nim` This is a workaround to fix this error: https://travis-ci.com/hdashnow/STRling/builds/140315052 But means version needs to be updated in two places each time, so would be nice to fix.

By default only output loci passing certain filtering thresholds e.g. number of anchored or spanning pairs. Have a flag to output all loci.

`strling call -f g1k_v37_decoy.fa -l loci.hg19.bed -o hg002.extra hg002.cram hg002.str.bin` If chromosome names in `loci.hg19.bed` above don't match the reference genome (e.g. chr 1 vs 1) then the following error...

E.g. less than 4 soft-clipped reads each side

It would be extremely useful to report the MC on the reference allele. This could go in the INFO. This would enable us to detect repeat differences from the reference...