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Call SNPs and indels from aligned reads using bcftools mpileup and call.
Passed 23 of 23 test cases with the skill, and 21 of 23 without it.
2 fixed21 passed either way0 still failing0 broke
Tokens, turns and time describe resource use, not a dollar price.
One of 2 test cases the skill fixed. Same model, same prompt, with and without the skill.
When running variant calling across non-standard sex chromosomes or variable ploidy regions in `sample.bam`, I have created a definition text file `ploidy.txt`. Which flag should be supplied to the calling subcommand to apply this custom ploidy file?
| Checked | Without skill | With skill |
|---|---|---|
| Specifies --ploidy-file ploidy.txt during the calling command. | Missed | Passed |
The instructions your model reads when the skill loads.
Call SNPs and indels from aligned reads using bcftools.
BAM file + Reference FASTA
|
v
bcftools mpileup (generate pileup)
|
v
bcftools call (call variants)
|
v
VCF file
bcftools mpileup -f reference.fa input.bam | bcftools call -mv -o variants.vcf
test cases passed, vs 21 / 23 without
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