different bam from same NGS data
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4.2 years ago
gab ▴ 20

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?

bam bwa • 760 views
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are you using the same parameters/software/ remove duplicates etc... ?

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

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And that you aligned to the same reference?

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Yes, same exact file fasta

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4.2 years ago
jsporter ▴ 60

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.