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?
