Should we use BAQ model when detect variants sites?

[biozzq]

Dear all,

In order to compare with GATK, I also called the variants using ANGSD with following command which can report the homozygous for alternative alleles. But I found the ANGSD have excluded many sites which can be high quality in GATK. But when I ran without BAQ model, the variants detected by ANGSD and GATK will have a high overlapping rate. So I want to know when should we run use BAQ when running ANGSD.
angsd -bam $list -only_proper_pairs 1 -uniqueOnly 1 -remove_bads 1 -minQ 20 -minMapQ 30 -C 50 -ref reference.fa -baq 1 -r $chr -out $chr -doMaf 1 -minInd $min -skipTriallelic 1 -doMajorMinor 4 -GL 1 -setMinDepth $mindepth -setMaxDepth $maxdepth -doCounts 1 -P 5 -doGlf 2 -SNP_pval 1e-6

Best
zhuqing

[claudiuskerth]

Hi Zhuqing,

I think it is advisable to apply BAQ when using ANGSD. GATK does not apply BAQ anymore because they do local re-assembly around candiate variable sites, which handles false-positive SNP's around indels better than BAQ does. Also note, that ANGSD provides two versions of BAQ: standard with baq 1 and extended with baq 2, the latter being more permissive than the former. Some more details can be found in this thread: #97.

claudius

[biozzq]

Dear @claudiuskerth

Many thanks. I think the baq 1 should improve more for the accuracy of SNP discovery but with a reduced sensitivity when compared with baq 2, Is this right?

Best
Zhuqing

[claudiuskerth]

Yes, Zhuqing,I think you are right. That's what I have read in forum posts by Heng Li (the author of BAQ). BAQ 2 (or "extended BAQ") as far as I understand should be more sensitive at the cost of accuracy. So more detected SNP's but also more false positive SNP's as compared to BAQ 1. I currently use BAQ 2, because my impression has been that BAQ 1 could lead to too many false negatives. I also get a much better looking site frequency spectrum with BAQ 2 as compared to BAQ 1.

claudius

[biozzq]

Dear @claudiuskerth
Thanks for your information.

Best
Zhuqing