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Old 03-19-2018, 06:21 AM   #1
iltisanni
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Location: Mainz, Germany

Join Date: Mar 2017
Posts: 20
Default SNPs detected in spades Assembly

Hi,

we assembled one 150bp paired-end illumina sample with spades 3.10 and got about 400 contigs with a size of > 1kb.

Afterwards we scanned for SNPs with samtools/varscan with the same fastq-files in the assembly made out of these.
I know this doesn't make much sense :-), but samtools called some SNPs and we can see them in IGV, so they are really there.

How is this even possible, that we find a SNP with the same fastq files, of which the assembly is made of?

Last edited by iltisanni; 03-20-2018 at 04:02 AM.
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