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Step 3: Filter and report the incorrect directory in hightlight section
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In step 3 of Variant calling in the section called filtering beginning at line 265 on the github script, where we compare the quality of the of the variants called before and after filtering, the directory name is wrong when running the unfiltered variants. 
Line 274 currently has /bcf/ instead /vcf/.
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Hanson19 authored Jan 9, 2024
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Expand Up @@ -271,7 +271,7 @@ calculating the ratio of [transitions(TS)](https://en.wikipedia.org/wiki/Transit
where transitions should be more likely to occur than transversions:

```bash
$ bcftools stats results/bcf/SRR2584866_variants.vcf | grep TSTV
$ bcftools stats results/vcf/SRR2584866_variants.vcf | grep TSTV
# TSTV, transitions/transversions:
# TSTV [2]id [3]ts [4]tv [5]ts/tv [6]ts (1st ALT) [7]tv (1st ALT) [8]ts/tv (1st ALT)
TSTV 0 628 58 10.83 628 58 10.83
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