Glcomparison

For some analysis the choice of GL model will make a huge impact, this is shown in the example where we estimate the sfs using -GL 1 and -GL 2, for two list of BAM files downloaded from the 1000genomes project website. First list are 12 CEU samples from 2011, and second list are the same 12 CEU samples but from 2013.

Below are the commands used

angsd -b new.list -minQ 20 -minMapQ 30 -isBed 1 -sites 1kg.accesible2.gz -GL 1 -out res/new.list.gl1 -doSaf 1 -r 1: -anc hg19ancNoChr.fa -P 6
/home/thorfinn/angsd/angsd -b new.list -minQ 20 -minMapQ 30 -isBed 1 -sites 1kg.accesible2.gz -GL 2 -out res/new.list.gl2 -doSaf 1 -r 1: -anc hg19ancNoChr.fa -P 6
/home/thorfinn/angsd/angsd -b old.list -minQ 20 -minMapQ 30 -isBed 1 -sites 1kg.accesible2.gz -GL 1 -out res/old.list.gl1 -doSaf 1 -r 1: -anc hg19ancNoChr.fa -P 6
/home/thorfinn/angsd/angsd -b old.list -minQ 20 -minMapQ 30 -isBed 1 -sites 1kg.accesible2.gz -GL 2 -out res/old.list.gl2 -doSaf 1 -r 1: -anc hg19ancNoChr.fa -P 6