BAM file statics and heterozygoty rate
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.
• 2,995 views
•
link
updated
by
Gabriel R.
•
written
by
kk.mahsa
•
written
by
kk.mahsa
1 answer
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
• 0 views
•
link
written
by
Gabriel R.
Log in to answer this question.
More posts like this
-
compare the assembler MaSuRCA and SPAdes for assembly unmapped reads
written by Sony Nguyen •
-
find position of snps in cM, given recombination map from ldhelmet
written by Jautis
-
calculate Per variant Heterozygosity from VCF file
written by SOHAIL
-
calculate Per variant Heterozygosity from VCF file
written by SOHAIL
-
Understanding de-novo transcriptome assembly quality using Transrate
written by nayaraevelin2 •
-
de-novo whole genome assembly and annotation
written by kratiranjan2020 •
-
How to decide the --min-covered-fraction value In PoPoolation?
written by mariacavedon2 •
-
How Coverage percentage is calculated in NGS data
written by crivenster
-
Total Length Of Assembled Scaffolds Is Greater Than Genome Length
written by AW
-
Gene Coverage In Music
written by yliubu •
