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Quick Start & Test Dataset

Step by step genotyping tutorial



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BisSNP Input example files

Download necessary reference genome hg18 and dbSNP file here, then use the following test BAM file and interval file for the testing:

BisSNP Output example files

You would get snp.raw.vcf and cpg.raw.vcf by default output mode. genotype.raw.vcf contains all of the confidant called sites' genotype when specify output modes with EMIT_ALL_CONFIDENT_SITES.

BisSNP quick start

Download the reference genome hg18 file, dbSNP file, input example bam files and interval file, put them into the same directory with BisSNP.jar. Unzip the *.bz2 files. Run the following commands.

  • java -Xmx4g -jar BisSNP-0.71.jar -T BisulfiteGenotyper -R hg18_unmasked.plusContam.fa -D dbsnp_135.hg18.sort.vcf -I normalMerge_chr11-7M-9M.nodups.withhead.bam -vfn1 cpg.raw.vcf -vfn2 snp.raw.vcf -stand_call_conf 30 -stand_emit_conf 0 -L Interval_list-test.bed

Finally, run vcf2bed.pl like this, you could get extended bed file contained cpg methlation value.

  • perl vcf2bed.pl cpg.raw.vcf CG

For visulization, run vcf2wig.pl or vcf2bedGraph.pl, you could get homozygous CpGs' wiggle track/bedGraph file.

  • perl vcf2wig.pl cpg.raw.vcf CG

 

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