GATK4, BaseRecalibrator, Known site, Drosophila

Question

[wjddn216]

Hello

I study a GATK4 - BaseRecalibrator and I use the drosophila sequence for practice.

I didn't find a drosophila known-sites, can you share me link that have a drosophila known-sites ?

(Example)

gatk BaseRecalibrator \
   -I my_reads.bam \
   -R reference.fasta \
   --known-sites sites_of_variation.vcf \
   --known-sites another/optional/setOfSitesToMask.vcf \
   -O recal_data.table

Thank you

-CJ-

Answer 1

[wjddn216]

I found a drosophila snp vcf from here.

http://www.iipl.fudan.edu.cn/FlyVar/sourcefordownloading.jsp

-CJ-