fix: add sd_locs_vcf_index input to SDtoBAF

[simojoe]

Fixes #643

Adding the index in-place from the main file name.

I have not found any other reference to SDtoBAF that needs to be updated.

[VJalili]

@simojoe, thank you for fixing this! Optional index files can be confusing, and your suggested fix fits perfectly with what we discussed in #578.

I want to suggest an improvement on your approach; can you please add an optional input sd_locs_vcf_index to the WDL, such that, if sv_locs_vcf is given, the sd_locs_vcf_index should also be given, and if sd_locs_vcf_index is not given, then infer it from sv_locs_vcf.

[mwalker174]

Thanks @simojoe. I was at first surprised since we haven't seen this before but then noticed you are using the gzipped version of the dbsnp vcf. We currently reference the uncompressed version, which is why it didn't require an index. Unfortunately, if we ran your change with the uncompressed version it would fail because its index does not have a .tbi extension:

> gsutil ls "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf*"
gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf
gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf.gz
gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf.gz.tbi
gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf.idx

I think we should be using the compressed one instead, but this will affect the code base in 2 other places:

• Needs index file input:

  gatk-sv/wdl/CollectSVEvidence.wdl

  Line 57 in 0cad166

  File sd_locs_vcf

• Update to the .gz file:

  gatk-sv/inputs/values/resources_hg38.json

  Line 15 in 0cad166

  "sd_locs_vcf" : "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf",