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change the output directory for vcf to vcf
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`$ bcftools call....` command's output is in vcf format but the output path is pointing to the bcf directory. Direct it to vcf to avoid confusion :)
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DininduSenanayake authored Aug 5, 2021
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2 changes: 1 addition & 1 deletion episodes/04-variant_calling.md
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Expand Up @@ -256,7 +256,7 @@ We have now generated a file with coverage information for every base.
Identify SNPs using bcftools `call`. We have to specify ploidy with the flag `--ploidy`, which is one for the haploid *E. coli*. `-m` allows for multiallelic and rare-variant calling, `-v` tells the program to output variant sites only (not every site in the genome), and `-o` specifies where to write the output file:
~~~
$ bcftools call --ploidy 1 -m -v -o results/bcf/SRR2584866_variants.vcf results/bcf/SRR2584866_raw.bcf
$ bcftools call --ploidy 1 -m -v -o results/vcf/SRR2584866_variants.vcf results/bcf/SRR2584866_raw.bcf
~~~
{: .bash}
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