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missing SNPs after gvcf combine and slow combination step
Hi, I'm using GATK ver 3.4 for SNP calling and I have some question about it. My data set has 500 samples, and I used genome data as reference for bowtie/GATK
1) I called SNP by sample (gvcf) with haplotype and then combined gvcf, however, the combination takes a long time, the GATK wants to recreate gvcf.idx files (4 of my gatk mission stuck at this step), one gatk combination finished after about 20 days calculation. I also try to use '-nct' to improve this, but it still stuck at preparing idx files.
2) For that finished gatk combination data set, I also used Unifiedgenotype with Gr.sorted.bam as input to call SNPs. The result is output with Gr.sorted.bam has 5 times more SNPs number than gvcf combination, and most missing SNPs could be found in individual gvcf files but missing in final result.
Could you help me with these? Thank you!