local heterozygosity with sliding windows

[dfguan]

Hello, I was trying to calculate local heterozygosity with sliding windows. I did this by generate those windows with awk and piped them to realSFS using xargs, and used SFS to get local heterozygosity. However I found this is very slow, it has run for days. So I am wondering if there is a fast way of calculting local heterozygosity.

Thanks in advance, Dengfeng.

[ANGSD]

Can you supply me with the commands you have used?

On 20 Aug 2021, at 09.38, Dengfeng Guan @.***> wrote:

Hello, I was trying to calculate local heterozygosity with sliding windows. I did this by generate those windows and piped them to realSFS, and used SFS to get local heterozygosity. However I found this is very slow, it has run for days. So I am wondering if there is a fast way of calculting local heterozygosity. Thanks in advance, Dengfeng.

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[dfguan]

Thanks for your quick reply. Here is the command, faidx is the index of ancestral genome fasta, and saf_idx is the index generated by angsd:

cut -f1,2 faidx | awk '{for(i=1; i < $2; i+=10000) print $1":"i"-"i+50000}' | xargs -n1 -i realSFS $saf_idx -r {} > est_local.SFS

Best, Dengfeng.

[ANGSD]

Can you also supply me with the angsd and realSFS commands.

On 20 Aug 2021, at 13.38, Dengfeng Guan @.***> wrote:

Thanks for your quick reply. Here is the command, faidx is the index of ancestral genome fasta, and saf_idx is the index generated by angsd:

cut -f1,2 faidx | awk '{for(i=1; i < $2; i+=10000) print $1":"i"-"i+50000}' | xargs -n1 -i realSFS $saf_idx -r {} > est_local.SFS Best, Dengfeng.

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[dfguan]

Here are the angsd and realSFS commands:

angsd -i $bam -anc $fasta -dosaf 1  -GL 2 -doCounts 1 -doMaf  -out $example 
cut -f1,2 $fasta.fai | awk '{for(i=1; i < $2; i+=10000) print $1":"i"-"i+50000}' | xargs -n1 -i realSFS $example.idx -r {} > est_local.SFS

Dengfeng.