How to select BAM files for contamination estimation?

[StuYuXu]

Hello, this is very good software. Thanks to you for developing it. However, I have a question, and I hope to get your help.

As the principle of your software, there are two parts: one performing damage-based contamination estimation and the other utilizing a database of mitochondrial allele frequencies.

So, does that mean I need one original bam (contained terminal damage information bam) for the first step? Then I use the trimmed bam (cut 10 bp to remove terminal damage bam) for the second step.

As I noticed, if I only used original bam (contained terminal damage information bam) for these two steps, the consensus sequence of my data was called contained terminal damage information. Thus, might it influence the results?

So, I hope you can help me with this problem!

Student,

Yu Xu

[grenaud]

schmutzi handles damage internally and this is what powers the inference. You do not need to trim anything just map your ancient DNA fragments to the mitochondrial genome in isolation

[StuYuXu]

Thanks for you sincerely response.
I successfully used your software to get the contamination estimation.

contDeam.pl --library double --out sample_1 sample_1.mapped.bam_MT.MD.bam
schmutzi.pl --t 30 --qual 30 --uselength --ref hs37d5_MT.fa sample_1 ./eurasian/freqs/ sample_1.mapped.bam_MT.MD.bam

[grenaud]

great, but beware that contDeam only gives you a ballpark estimate and there are a lot of assumptions in there. the iterative approach is the way to go :-)