Question: different bam from same NGS data
0
gravatar for gab
9 weeks ago by
gab20
gab20 wrote:

I was given some bam files I used to call somatic variants. The high number of SNP and mutations i found seemed suspicious, so I asked for the original fastq files to redo the allignment. While waiting for them I tried to get fastq from those bam files using bedtools bamtofastq . I used bwa mem to check allignment and the new bam file yeld less mutations and SNPs. Is there a procedure I didn't understand in the bedtools function that might have given me a fastq file different than the original?

bwa bam • 169 views
ADD COMMENTlink modified 9 weeks ago by jsporter60 • written 9 weeks ago by gab20
1

are you using the same parameters/software/ remove duplicates etc... ?

ADD REPLYlink written 9 weeks ago by Pierre Lindenbaum117k

I guess so, although I'm still waiting for the guy who did the first analysis to reply

ADD REPLYlink written 9 weeks ago by gab20
1

And that you aligned to the same reference?

ADD REPLYlink written 9 weeks ago by swbarnes24.9k

Yes, same exact file fasta

ADD REPLYlink written 9 weeks ago by gab20
1
gravatar for jsporter
9 weeks ago by
jsporter60
jsporter60 wrote:

The BAM file will not necessarily include the whole read from the original FASTQ file since it can be clipped, and this could lead to different alignment results.

ADD COMMENTlink written 9 weeks ago by jsporter60
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