compare CLC SNP's with dbSNP

[boetsie]

Hi all,

we did exome sequencing using the Nimblegen SeqCap EZ Exome SR protocol and obtained reads from Illumina GAIIx. We have analyzed our data for SNPs with CLC by mapping all the reads to the 24 human genomes (NC_000001 till NC_000024) and included the target regions in the annotations.

Now I have a table with SNPs which I want to compare with dbSNP. My results from CLC look something like this;

Mapping Reference Position Consensus Position Variation Type Length Reference Variants Allele Variations Frequencies Counts Coverage Variant #1 Frequency of #1 Count of #1 Variant #2 Frequency of #2 Count of #2 Overlapping Annotations Amino Acid Change
NC_000001 mapping 801943 9625 SNP 1 C 1 T 100 121 121 T 100 121 Primary_target_region: Primary_target_region, Capture_target: Capture_target
NC_000001 mapping 14930 526 SNP 1 A 2 G/A 69.0/31.0 29/13 42 G 69.048 29 A 30.952 13 Gene: WASH5P


I've downloaded a dbSNP file from UCSC;

http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/snp131.txt.gz

and looks like this;

bin chrom chromStart chromEnd name score strand refNCBI refUCSC observed molType class valid avHet avHetSE func locType weight
585 chr1 10433 10433 rs56289060 0 + - - -/C genomic insertion unknown 0 0 near-gene-5 between 1

Does anyone know how to compare the CLC SNPs with the SNPs in the dbSNP file? In addition, should I rename the CLC SNP file chromosomes (NC_000001 - NC_000024) to (chr1 - chrY) or should i rename the chromosomes from dbSNP the opposite way?

We will have many exome sequencing coming up and want to have a quick and easy pipeline. What is the best way to do this with CLC, or should we use another program for this?

Kind regards,
Boetsie

[kopi-o]

Try to annotate your reference genome with the dbSNP file in the CLC Bio software. After you have done this once, your SNPs will be automatically cross-checked against dbSNP (given that you use this annotated reference genome).