Obtaining SNPs with large samples in a short time

Question

[Daier]

Hi I have 150 samples. Now I have completed the mapping step and got the final BAM file. At present, I need to call SNP. Using angsd software, but has not been successful (run was killed), do not know what reason. I also learned that samtools and gatk software can call SNP, but it will take at least a month. So what other software can call SNP for a large number of samples in a short time?

[Kevin Blighe]

These are whole-genome BAMs? Please add more information

[Daier]

Yes, they're all whole-genome BAMs.

Answer 1

[Pierre Lindenbaum]

Create a GVCF file for each samples in a 'small genomic region" with gatk haplotypecaller in GVCF mode, Combine the GVCFs with gatk CombineGVCFs and create the final vcf with gatk GenotypeGVCFs.

...see the "GATK best practices".

Answer 2

[Qiongyi]

I totally agree with what Pierre recommend above. It definitely won't take a month if you know how to go through the GATK workflow. I would say a couple of days for WGS data. To speed it up, you can also split your regions of interested into many smaller BED files (e.g. split the whole genome BED to chromosome-level BED) and run jobs in parallel.

[Alex Reynolds]

To split a sorted BED file, here is an efficient way to do that:

$ for chr in `bedextract --list-chr input.bed`; do bedextract $chr input.bed > input.$chr.bed; done

This will be several times faster than awk or other approaches.