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Regarding Gatk output
I want to identify snps in my sequencing data.I am new in this field so i am just following guideline that you provided. i have paired end sequencing data (one sample) and according to documentation. i ran the programs and in the end i ran
java -Xmx32g -jar GenomeAnalysisTK.jar -T HaplotypeCaller -R genome.fasta -I realigned.bam -nct 14 -stand_call_conf 30 -o DK_new.vcf
After getting vcf file, i want to filter vcf file on the basis of allelic depth (DP) that describe in format column. Can you tell me how can i do this.
One more question about the DP value.. why DP value is different in info and format column???
i read the discussion about this and find that because of informative reads and uninformative reads. So it will always possible that allelic depth < total read depth at particular site. so it will better that to filter snps on basis of allelic depth than the total read depth.
I am totally confused that how can i filter snps ????
Please give suggestions about that.
Thanks & Regards