Hi all,

Since GATK HaplotypeCaller takes long time to genotype given SNPs using GGA mode (--alleles), I want to switch to freebayes to get the SNP genotypes.

I followed the tutorial from Freebayes Github, but it did not work as expected.

The command I used is "~jjiang/program/freebayes/bin/freebayes -f /bioinfo/data/iGenomes/genome.fa -@ wellwise_extract_snps.vcf.gz /data/NGS/WW20170913G01-1920094067/analysis/align/GWI281_combined.bam"

VCF file was gziped and indexed with tabix as suggested.

vcf file was zipped using bgzip command and then indexed with tabix.

$zcat wellwise_extract_snps.vcf.gz

fileformat=VCFv4.0

Time=20170921

Total_snps=2016

Version=1.5

CHROM POS ID REF ALT QUAL FILTER INFO

10 135339605 rs3813867 G C . . .

13 32903605 13:g.32903605delTG CTG C . . .

13 32905141 rs80359671 ACAAAT A . . .

13 32907409 rs276174813 CATCTT C . . .

13 32914974 rs770263702 AACAA A . . .

13 32954003 13:g.32954003delAACA TAACA T . . .

13 32954050 rs28897756 G A . . .

Y 2657442 rs748877650 T G . . .

There are 10 SNPs in the gzipped vcf file, therefore, I expected to see 10 exact SNP in the output file.

However, freebayes output all variants in the bam file. It seems that the -@ option did not work at all.

And I also tried adding -l option to force the genotyping. But it did not work either.

Any one can give me some suggestion?