Update README.md

day3_SV/README.md

@@ -147,15 +147,13 @@ In the second line, `1	156526704` indicates that the first breakpoint is at chr1
 
 Therefore, Delly generated the same results from `chr1.2mb.bwa.bam` and `chr1.2mb.mp2.bam`. 
 
-Generally speaking, to find overlaps between a set of regions and another set of regions, more specialized tools such as BEDtools or ANNOVAR can be used. However, since we are only looking at one single deletion, it is easy enough to just dig through the VCF file generated by Delly.
-
-However, in addition to this particular deletion, Delly generated many more SV calls on either BAM files. We can do some more investigation here. Using `bcftools`, we can see that there are 43 SV records in the first file and 117 records in the second file. Many such records have a FILTER called LowQual. To check this we can use the command below:
+However, in addition to this particular deletion, Delly generated many more SV calls on both BAM files. We can do some more investigation here. Using `bcftools`, we can see that there are 43 SV records in the first file and 117 records in the second file. Many such records have a FILTER called LowQual. To check this we can use the command below:
 
 ```
 bcftools query -e'FILTER="."' -f'%CHROM %POS %FILTER\n' chr1.2mb.bwa.bam.delly.bcf
 ```
 
-We can see that there are only 7 SV calls that have PASS as the filter.
+We can see that there are only 7 SV calls that have PASS as the filter. Next, we want to generate a new SV call set with filtered calls (with higher confidence).
 
 ```
 bcftools filter -e 'FILTER="LowQual"' chr1.2mb.bwa.bam.delly.bcf -Ob -o chr1.2mb.bwa.bam.delly.filter.bcf