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Old 06-04-2018, 12:44 AM   #1
Dr. Deepak
Junior Member
 
Location: Delhi

Join Date: Aug 2015
Posts: 3
Lightbulb GATK SNP multi-sample without known SNP database ?

I am working on identifying the SNPs in the genome of an insect which is sequenced in three samples. Following the GATK best practice pipeline i have completed the following task.

Quality filtered reads.
Read Alignment for each sample eg. S1, S2, S3.
Sort and mark duplicates in each sample S1, S2, S3.
Realign target and Indel realinger on each sample S1, S2, S3. Now i am stuck with next steps. As it require the base recalibration (BSQR) step. which require the known database of snps. however i dont have any known snp database so i am following the alternative steps mentioned the GATK for non-model organism. That is
I call the raw SNPs in gvcf model from each sample and then make joint calling for a final combined vcf file.
Next, I applied the hard filters on this file and extract good quality SNPs and indels as a reference database of BSQR step.

Now the question is i have three realigned files S1_realigned.bam, S2_realigned.bam, S3_realigned.bam from step 4 and a reference database of SNP and Indels (if i am right) from the step 6. So how i would proceed further. Did i use against each sample separately or make a combine re-calibration table by providing all three in the same command.
Thanks Dr. Deepak
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base recaibration, gatk, snp call

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