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:

• normalMerge_chr11-7M-9M.nodups.withhead.bam (57M, md5: 36d6ba2499f96deedfcc2d879b224aa4)
• normalMerge_chr11-7M-9M.nodups.withhead.bam.bai (9.5K)
• Interval_list-test.bed (1K)

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.

• genotype.raw.vcf (14M)
• snp.raw.vcf (45K)
• cpg.raw.vcf (233K)

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