Hi GATK Users,

Happy Thanksgiving!
Our staff will be observing the holiday and will be unavailable from 22nd to 25th November. This will cause a delay in reaching out to you and answering your questions immediately. Rest assured we will get back to it on Monday November 26th. We are grateful for your support and patience.
Have a great holiday everyone!!!

Regards
GATK Staff

Regarding Gatk output

Hello,
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

Answers

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