BAM file statics and heterozygoty rate

Question

[kk.mahsa]

i have two question and hope to help me

1- what program or script can calculated assembly coverage (as the proportion of bases in the genome assembly that were covered by at least one read) from BAM file?

2- how do i calculate heterozygosity rate in re-sequencing studies? i get number of heterozygote SNPs and length of reference genome. In denovo assembly studies, heterozygosity rate calculated as "number of Het SNPs / length of assembled genome(bp)" but i am not sure about in re-sequencing studies.

Answer 1

[Gabriel R.]

1- "samtools depth" could help you. I recommend using a bed file with mappable regions.

2- have you tried ANGSD:

http://www.popgen.dk/angsd/index.php/Thetas,Tajima,Neutrality_tests