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16 months ago
wonde2000
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0
I am working on WGS on bos indicus using ARS-UCD1.2 reference genome. However, I have no idea where to download known sites (indels and dbSNPs in vcf format) for base quality recalibration in GATK. Is there any one who would suggest me the link? thank you in advance for your precious time and considerations.
You can find the GVF format file for bos variants on Ensembl site: https://ftp.ensembl.org/pub/release-108/variation/gvf/bos_taurus/
You will need to convert the GVF file to VCF format using a script linked in this answer: Convert GVF to VCF
Thank you so much. I got it.
Dear GenoMax, Thank you for your prompt response. I got 1000 bull BQSR in this link https://sites.ualberta.ca/~stothard/1000_bull_genomes/?C=D;O=A
I think this is the better way to use it for BQSR. Does this should be used in .gz format as it is or unzip it? and this BQSR is used to recalibrate both indels and SNPs? is it necessary to index it before I use for base recalibrations? Finally, what is the purpose of .tbi file for the same BQSR and mandatory to download it? Thank you!
Dear All, I hope you all are doing well. Known sites (dbSNPs and Indels) are required to do BQSR. As GenoMax suggested me, I try to change bos_taurus.gvf.gz to bos_taurus.vcf.gz but I couldn't succeeded (i.e. the site GenoMax suggested is not working for me). Therefore, I sincerely request your immense help as usual. I know you have very busy schedules, but thank you in advance for your unwavering support!
here is the bos_taurus.gvf.gz site https://ftp.ensembl.org/pub/release-108/variation/gvf/bos_taurus/