Commit 550d92ac authored by Beatriz Vicoso's avatar Beatriz Vicoso
Browse files

Update ancestrySNP.md

parent 61741dfa
......@@ -140,6 +140,11 @@ cat head_filtered.vcf | awk '(($10 ~ "0/0" && $11 ~ "0/0" && $12 ~ "1/1" && $13
--> 600233 SNPs
Subset so we keep only F2 samples in the VCF:
```
bcftools view -s asex1.bam,asex2.bam,asex3.bam,asex4.bam,asex5.bam,sex1b.bam,sex2b.bam,sex3b.bam,sex4b.bam,sex5b.bam,sex6b.bam,sex7b.bam,sex8b.bam,sex9b.bam,sex10b.bam head_filtered_fixedSNP.vcf > head_filtered_fixedSNP_sexAsex.vcf
```
# check number of individuals that carry heterozygous alleles
Since we start the cross with diverged individuals, we expect that many sites will be heterozygous in ~50% of F2 females. Let's check if this is the case.
......
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