BisSNP Files

Change log
2018-2-24
BisSNP-1.0.0:
-adapt to GATK3.8.1 framework, allow to run on Java 8 in both of oracle and openJDK.
-allow input of dbSNP VCF file as gzipped and tabix indexed file
-fixed some bugs in bisulfite conversion filters
-add a lot of new walkers for the bisulfite QC
-should not to specify -stand_emit_conf
-source code is moved to Github: https://github.com/dnaase/Bis-tools/tree/master/Bis-SNP
-source code is compiled and managed by maven now.

2013-7-2
BisSNP-0.82.2, add an option (-notEncrypt) to output raw read ID into cpgreads files, which may cause the file to be very large.

2013-6-19
BisSNP-0.82, enable to output hcgreads/gchreads for NOMe-seq. fix bugs on reference cytosine pattern output in VCF file.

2013-2-26
BisSNP-0.81, fix a memory leak bug during the multithread output.

2013-2-1
BisSNP-0.80, enable the output of low quality CpGs and reference CpGs(not called as CpG) in cpg.raw.vcf file. Fix the bug for wrong alleles display when there are try or more alleles. Fix the bug that call CpH methylation status improper on non-directional protocol BS-seq.

2013-1-4
BisSNP-0.78, fix a bug for paired-end's second end base quality score recalibration. previous version has the problem that over-estimate the mismatch rate in 2nd end base. This improvement would improve a lot on SNP calling in paired-end data.

2012-12-6
BisSNP-0.77, enable genotype in non-directional protocol by using command "-nonDirectional". Optimize the prior calculation in dbSNP position, add GMAF in dbSNP for more accurate prior estimation, which will benefit non-directional or one strand only bisulfite-seq. Add the feature that only output heterozygous SNPs in dbSNP position in "-cpgreads" mode. 

2012-12-3
BisSNP-0.76.1, fix the "java.lang.NullPointerException" bug in BisSNP-0.76, which is an internal version been released by accidentally…

2012-11-6
BisSNP-0.76, in paired end sequencing, when pair of reads are overlapped with each other, get rid of both of them when the base call or methylation status disagree, or get rid of the bad base quality one when they agree with each other.

2012-11-2
BisSNP-0.75, add summarize of the coverage information in different region. User could provide a bed file, like CpG islands, then the summary output would calculate the average coverage in these regions and the whole genome.

2012-10-23
BisSNP-0.74, enable output of heterozygous SNPs allele in -cpgreads mode, so allele type with read name will also be output in haplotype.txt file, which will be convenient for allele specific methylation analysis. All CpGs output in haplotype.txt file will be just homozygous CpGs.

2012-08-23
BisSNP-0.73, allows to remove 5' or 3'end n bp of the reads for the genotyping and methylation calculation. User can use '-trim2nd' to enable the trimming only on 2nd end reads (Paired end sequencing) for tagmentation-based whole genome bisulfite sequencing. 

2012-08-14
Bis-SNP 0.72, fix a bug for genotype field output in multiple samples input mode. Thanks for Lei Gu's bug report!

2012-08-13
Bis-SNP 0.71.1, fix a bug for String comparison bug in SortingVCFWriterOwnBase class, when running BisSNP with GRch37 reference genome in parallel mode. Thanks for Lei Gu's bug report!

2012-07-23
Release bissnp_easy_usage.pl, it provides an easy and integrated way to use BisSNP pipeline. It includes indel realignment, mark duplicate reads, base quality score recalibration, genotyping, SNP filtering, VCF to bed steps. For usage of bissnp_easy_usage.pl, please run "perl bissnp_easy_usage.pl" in terminal

2012-07-23
Update SortByRefAndCor.pl. Fix the bug that incorrectly place VCF file header after the sorting.

2012-07-22
Bis-SNP User Manual v_001(For Bis-SNP 0.71) released.

2012-07-13
Bis-SNP 0.71 Released, which is the formal released version.