Dear Miller,

Thanks so much for you reply so quickly, I will try this bam-readcount to pull VAFs from both bam.

One more question: for your CNV segment file, I found those distance of segment windows are so diverse in different chromosome:

chr1 1 351000
chr1 351001 650000
chr2 1 215000
chr3 1 500000
...

I just wonder which tools you used? Actually, I use VarScan, Conifer and CNVkit to call CNV, segmented by DNAcopy. but when I got segment CNV should I convert by Bedtools -w 50k (or other num) to make window distance, and re-calulated again? or just used DNAcopy segment CNV as input file for sciclone? before input to sciclone should I remove those CNV changed region or I can give all the info to sciclone, later use copyNumberMargins=0.25 to filter out?

Also I saw you CNV segment value already changed back to real CNV copy number: like (2^0.5)*2, but in R script still use

 copyNumberMargins=0.25

Thanks for you help and your tools are really really nice and help our team a lots. Haitao

Dear Chris,

I'm following what you mentioned in this post, I got bam-readcount output file now:

GL456392.1      772     C       123     =:0:0.00:0.00:0.00:0:0:0.00:0.00:0.00:0:0.00:0.00:0.00  A:0:0.00:0.00:0.00:0:0:0.00:0.00:0.00:0:0.00:0.00:0.00  C:103:30.22:36.83:1.46:46:57:0.57:0.06:145.63:46:0.46:64.46:0.33        G:0:0.00:0.00:0.00:0:0:0.00:0.00:0.00:0:0.00:0.00:0.00  T:20:31.10:37.00:0.00:11:9:0.78:0.09:182.55:11:0.59:55.90:0.34  N:0:0.00:0.00:0.00:0:0:0.00:0.00:0.00:0:0.00:0.00:0.00
GL456378.1      780     T       2       =:0:0.00:0.00:0.00:0:0:0.00:0.00:0.00:0:0.00:0.00:0.00  A:2:33.00:37.00:0.00:1:1:0.32:0.04:129.50:1:0.71:100.00:0.38    C:0:0.00:0.00:0.00:0:0:0.00:0.00:0.00:0:0.00:0.00:0.00  G:0:0.00:0.00:0.00:0:0:0.00:0.00:0.00:0:0.00:0.00:0.00  T:0:0.00:0.00:0.00:0:0:0.00:0.00:0.00:0:0.00:0.00:0.00  N:0:0.00:0.00:0.00:0:0:0.00:0.00:0.00:0:0.00:0.00:0.00

However, I don't know which tool can help me to convert bam-readcount output to like this VAF output:

chrom POS REF ALT REF_DP ALT_DP TOTAL_DP
GL456378.1 772 C A 103 20 123
GL456378.1 780 T A 0 2 2

Thanks in advance, Haitao

There are options like Theta that allow for merging that information back in, but no supported procedure for merging the two that I know of. You're welcome to invent one, as it's probably possible.

One way is to use something like VATools to annotate your VCF with that information, then extract it by parsing the VCF. https://github.com/griffithlab/VAtools