GATK pipeline for SNP calling from 454 GS-FLX sequencing data????

[Maulik23]

I want to call SNPs in GATK using the BAM file produced by GS Reference mapper , bu the problem with BAM file is it does not contain the read group so how to add read group in the bam file of 454 sequencing data and whether or not PICARD and GATK can be used to call SNPs from 454 sequencing data. Till now I was using samtools but now my task is to compare the output of Samtools and GATK. ANy help will be appreciated

[severin]

Gatk2.0

I want to call SNPs in GATK using the BAM file produced by GS Reference mapper , bu the problem with BAM file is it does not contain the read group so how to add read group in the bam file of 454 sequencing data and whether or not PICARD and GATK can be used to call SNPs from 454 sequencing data. Till now I was using samtools but now my task is to compare the output of Samtools and GATK. ANy help will be appreciated

The information you seek is out there in the help documentation. You will need to use Picard to add group information. I wrote a quick introduction to GATK2.0 here (http://gif.biotech.iastate.edu/blog/) I intend on following it up with my pipeline that i have created that takes in a same file and outputs a vcf file after going through bam conversion with samtooms, deduplication, sorting and read group addition with Picard and then GATK calling of SNPs. I have been using the new Haplotype caller which is slow unless you use it in parallel. The Queue system they have developed looks really powerful but I have had trouble implementing. I have found a work around and a way to load balance any genome for improved efficiency.

I will work on the next post so it makes more sense.

[Maulik23]

thanks for reply but my concern is with 454 sequencing data because I have not came across any good reference which has used GATK for SNP calling from Roche 454 sequencing data. Can you please brief me about the proper pipeline of SNP calling starting from adding of the read group to the variant calling in GATK using 454 sequencing data?