dbSNP & Indels files
dbSNP VCF files are downloaded from broadinstitute webpage and Sanger institute. we used sortRefAndCor.pl to sort with the reference sequence file's chromosome order which are required by BisSNP and GATK. Just for your convenience..
Reference genome files
The difference between hg19 and GRch37 is that GRch37 use the newest assembled chrM sequence(in GenBank with the record NC_012920), while hg19 use the older chrM sequence. We just add the newest chrM sequence to hg19, and add contamined sequence to hg18.
Whole genome interval files
You can also leave -L blank, then by default BisSNP will go over all of chromosome listed in BAM file header. You can also specify -L chr1 for each of the chromosome. chrY are still badly assembled and full of repeats yet, it is meaningless to call genotype there right now, so interval files here just provide autosome and chrX.
Useful scripts to deal with VCF files
The BisSNP output files are VCF files. These scripts could help you to convert it to bedgraph, wig or bed file for visualization or your own analysis.
- bissnp_easy_usage.pl (1K, Provide an easy way to use whole BisSNP genotyping pipeline)
- vcf2wig.pl (1K, Extract methylation information from VCF file to wiggle track)
- vcf2bedGraph.pl (1K,Extract methylation information from VCF file to bedgraph track)
- vcf2coverage.pl (1K, Extract cytosine covergae information from VCF file to bedgraph track)
- vcf2bed.pl (1K, Extract cytosine information from VCF file to UCSC extended bed format)
- vcf2bed6plus2.pl (1K, Extract cytosine information from VCF file to TCGA Bisulfite-seq level III extended bed format)
- BisulfiteAnalyzeCovariates-0.69.jar (8.7M, Analysis base quality score recalibration result, check User Manual for the usage)
- sortByRefAndCor.pl (1K, Sort VCF files by the coordinate and chromosome order provided in reference genome index file (e.g. hg19.fa.fai))