C2 several methods of merging VCF files

1. Individuals are the same , Locus accumulation , amount to cat file

vcf-concat A.vcf.gz B.vcf.gz C.vcf.gz | gzip -c > out.vcf.gz

vcf-concat *.vcf.gz | gzip -c > out.vcf.gz

2. Same locus , Individual accumulation , amount to paste file

bcftools merge file1.vcf.gz fle2.vcf.gz file3.vcf.gz > out.vcf

bcftools merge file1.vcf.gz fle2.vcf.gz file3.vcf.gz -o out.vcf

3. Different loci , Individuals are also different , Take two. VCF Intersection of documents

3.1 Use bedtools To operate

grep "#" A.vcf > header.txt grep -v "#" A.vcf | sed 's/Chr1/1/g' > temp.txt cat header.txt temp.txt > A_new.vcf bcftools isec -p isec_output -Oz A_new.vcf.gz B.vcf.gz

It turns out that isec_output In this folder , There are 4 File

1.isec_output/0000.vcf.gz would be variants unique to 1.vcf.gz 2.isec_output/0001.vcf.gz would be variants unique to 2.vcf.gz 3.isec_output/0002.vcf.gz would be variants shared by 1.vcf.gz and 2.vcf.gz as represented in 1.vcf.gz 4.isec_output/0003.vcf.gz would be variants shared by 1.vcf.gz and 2.vcf.gz as represented in 2.vcf.gz

Then get two VCF Common locus SNP

bcftools merge --merge all 0002.vcf.gz 0003.vcf.gz > merged.vcf

3.2 Use bedops To operate

This is the intersection of two files bed file ,region file

bedops --intersect <(vcf2bed < A.vcf) <(vcf2bed < B.vcf) > answer.bed

This is the intersection of two files bed file , Site file

bedops --intersect <(vcf2bed < A.vcf) <(vcf2bed < B.vcf) > common-regions.bed bedops --everything <(vcf2bed < A.vcf) <(vcf2bed < B.vcf) > all-elements.bed bedops --element-of 1 all-elements.bed common-regions.bed > common-elements.bed

This is to get the intersection of two files in A Variation and in B Variation in , This is an individual file

bedops --element-of 1 <(vcf2bed < A.vcf) <(vcf2bed < B.vcf) > answer1.bed bedops --element-of 1 <(vcf2bed <A.vcf) <(vcf2bed < B.vcf) > answer2.bed

4. Different loci , Individuals are also different , Take two. VCF Union of files

In response to this situation , The acquisition of union files requires two files bam file

grep -v "#" A.vcf | cut -f 1,2 > pos1.txt

grep -v "#" B.vcf | cut -f 1,2 > pos2.txt

cat pos1.txt pos2.txt > posAll.txt

After getting these two files , Later mpileup, Got the of each file mpileup Format files and then merge

samtools mpileup -A -B -q 20 -Q 20 -f ref.fa bamfile.bam -l posAll.txt -r -o

#! /bin/bash
# Use mpileup Command to generate vcf file 
# In this example, only 1 Chromosome was processed 
echo "SamtoolsMpileupByChr Begin: " `date` && \
samtools mpileup \
-l chr1Region.bed \
-r 1 \
-q 1 \
-C 50 \
-t DP,DV \
-m 2 \
-F 0.002 \
-f \
human.fasta \
test_3.bam \
--output test.chr1.raw.vcf && \
echo "SamtoolsMpileupByChr End: " `date`

mpileup Interpretation of the order

-C --adjust-MQ INT Coefficient used to reduce the quality of comparison , If reads There are too many mismatches in . Cannot be set to zero .BWA The recommended value is 50.

-A --count-orphans In detecting variation , Do not ignore abnormal reads Yes .

-I –positions FILE BED File or location list file containing regional sites . The location file contains two columns , Chromosome and location , from 1 Start counting .BED The file contains at least 3 Column , Chromosome 、 Start position and end position , Start end from 0 Start counting .

-r –region STR Only in the designated area pileup, Need indexed bam file . Usually and -l Parameters used together .

-q --min-MQ The minimum mapping quality of the alignment to use .

-f --fasta-ref FASTA Format fadix Index reference file . Files can be used optionally bgzip Compress .

-o –output FILE Generate pileup Format file or VCF、BCF File instead of the default standard output .

-g –BCF Calculate the likelihood value of genotype and the output file format is BCF.

-v –VCF Calculate the likelihood value of genotype and the output file format is VCF.

-D Output reads depth .

-V Output each sample that is not compared to the reference genome reads Number .

-t –output-tags LIST Set up FORMAT and INFO The contents of the list , Comma separated .

-u –uncompressed Generate uncompressed VCF and BCF file .

-I –skip-indel Don't test INDEL.

-m –min-ireads INT The candidate INDEL Minimum interval of reads.

-F –gap-frac FLOAT Contains intervals reads The smallest fragment of .