different bam from same NGS data

Question

[gab]

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?

[Pierre Lindenbaum]

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

[gab]

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

[swbarnes2]

And that you aligned to the same reference?

[gab]

Yes, same exact file fasta

Answer 1

[jsporter]

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.