--snp 根据vcf文件第三列ID列的snp名进行过滤。 --snps FILE,--exclude 根据ID文件进行过滤 变异类型过滤 --keep-only-indels --remove-indels 即保留或去除SNP,留下INDEL。 根据VCF文件第七列FILTER进行过滤 --remove-filterer-allFILTER列除了PASS保留,其余都过滤 --keep-filtered,--remove-filtered保留或去除...
SNP应仅由正向reads或仅反向reads涵盖。 vcffilter -f "SAF / SAR > 100 & SRF / SRR > 100 | SAR / SAF > 100 & SRR / SRF > 100" -s DP3g95p5maf05.fil1.vcf > DP3g95p5maf05.fil2.vcf 这次的过滤是基于比例,因此一些无关的reads不会删除整个基因座。简单来说,它保留的位点比反向交替rea...
ncludes or excludes all sites marked with a specific FILTER flag. These options may be used more than once to specify multiple FILTER flags.自己理解下就好 根据INFO过滤 –keep-INFO –remove-INFO Includes or excludes all sites with a specific INFO flag. These options only filter on the presence...
You can use VCFtools to filter out variants or individuals based on the values within the file. For example, to filter the sites within a file based upon their location in genome, use the options--chr,--from-bp, and--to-bpto specify the region. ./vcftools --vcf input_data.vcf --chr...
The resulting output file has the suffix '.snpden'. --TsTv <int> Calculates the Transition / Transversion ratio in bins of size defined by this option. The resulting output file has the suffix '.TsTv'. A summary is also supplied in a file with the suffix '.TsTv.summary'. --FILTER...
2 --max-alleles 2 \ --remove-indels 2>vcftools.log| gzip - >myresult/nohup1.vcf.gz & ...
Applying a filter Writing to a new VCF file Writing out to screen Converting a VCF file to BCF Comparing two VCF files Getting allele frequency Getting sequencing depth information Getting linkage disequilibrium statistics Getting Fst population statistics ...
larger structural variants, together with rich annotations. VCF is usually stored in a compressed manner and can be indexed for fast data retrieval of variants from a range of positions on the reference genome. The format was developed for the 1000 Genomes Project, and has also been adopted by...