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Fixed a few typos
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Gammerdinger authored May 31, 2024
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4 changes: 2 additions & 2 deletions lessons/08_variant_filtering.md
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Expand Up @@ -181,7 +181,7 @@ We can break this command down:
<hr />
</details>

In order **to remove the LCRs from the VCF file, we will once again be using `SnpSift`**. As we mentioned earlier, we will be discussing `SnpSift` at length in the [variant prioritization lesson](10_variant_prioritization.md), but for now were are going to focus on using the `intervals` command build into `SnpSift`. Let's go back to our scripts directory and edit our variant filtering script.
In order **to remove the LCRs from the VCF file, we will once again be using `SnpSift`**. As we mentioned earlier, we will be discussing `SnpSift` at length in the [Variant Prioritization lesson](10_variant_prioritization.md), but for now were are going to focus on using the `intervals` command built into `SnpSift`. Let's go back to our scripts directory and edit our variant filtering script.

Add the `filter` command from `SnpSift` to our `sbatch` script in order remove all sites that overlap with the BED file:

Expand Down Expand Up @@ -327,7 +327,7 @@ We can also check **how many variants are contained in our filtered file**:
grep -v "^#" /n/scratch/users/${USER:0:1}/${USER}/variant_calling/vcf_files/mutect2_syn3_normal_syn3_tumor_GRCh38.p7-pass-filt-LCR.vcf | wc -l
```

What this command does is use `grep -v` to search for lines in our filtered VCF that do *not* start with a `#` (and are therefore not comments, like we were looking at above, or the header row of the VCF), and then use `wc -l` to count the number of lines in that output.
What this command does is use `grep -v` to search for lines in our filtered VCF that do *not* start with a `#` (and are therefore not metadata, like we were looking at above, or the header row of the VCF), and then use `wc -l` to count the number of lines in that output.

We should see 1362 variants in our filtered VCF.

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