Quote Originally Posted by werno View Post
Hello,

I have analyzed my bam files with your tool bam-analysis-kit 1.8 und 2.0
and
I have found a discrepancy in the html SNPedia report for the Chr. 17.
I did not check others variations and chromosomes.

For example your tool found the following variations:

rs59328451
Location: 17:39766801
Your Genotype: TT
Summary: homozygote for pachyonychia congenita Type I mutation (more ..)

rs57424749
Location: 17:39768561
Your Genotype: CC
Summary: homozygote for pachyonychia congenita Type I mutation (more ..)

and in the SNPedia it is as follows, respectively

GenoMagSummary(A;A)0normal
(A;T)3heterozygote for pachyonychia congenita Type I mutation
(T;T)3homozygote for pachyonychia congenita Type I mutation



GenoMagSummary(C;C)3homozygote for pachyonychia congenita Type I
mutation
(C;G)3heterozygote for pachyonychia congenita Type I mutation
(G;G)0normal

According to these facts your tool evaluates the variations as
pathological but it is wrong. It seems that your tool does not check the
direction plus or minus orientation of the strand.

I have checked my data in IGV Viewer and
https://www.ncbi.nlm.nih.gov/snp and in my case these variants are not
pathological.

What do you think about this?
Snpedia analysis was written by the original author.

The second problem I have is, that bam-analysis-kit 1.8 und 2.0 can not
analyze the chromosomes 2, 9,19,20 in my bam files. For all bam files
always the same chromosomes. The bam files are from two different
institutes but maybe from the same machine but I do not have this
information. One bam file was created 4 years ago. Others last year. But
I have no problem e.g. with current samtools or GATK.
Would it be possible for you to share one of the BAMs and/or copy the output from BAM Analysis Kit.