elowy01 · October 31, 2025 16:13 · Jan 26, 2023 · Dec 6, 2022 · Jun 24, 2021 · Jun 6, 2019
diff --git a/BCFtools cheat sheet b/BCFtools cheat sheet
@@ -44,10 +44,7 @@ bcftools query -f '%CHROM\t%POS\t%INFO/DP\n' in.vcf.gz
 /
 0#printing a list of samples from a VCF:
 bcftools query -l test.vcf
-/
-#also, the FORMAT annotations can be obtained by:
-~/bin/bcftools/bcftools query -f '[%GT]\n' ../0002.vcf |wc -l #the GT in this case
-/
+
 *selecting snps from file:
 ~/bin/bcftools/bcftools view -v snps lc_bams.bcftools.20170319.NA12878.vcf.gz 
 /

diff --git a/BCFtools cheat sheet b/BCFtools cheat sheet
@@ -27,9 +27,6 @@ bcftools view -R 0002.tsv in.vcf.gz
 20      79000   80000
 20      90000   100000
 
-*printing out only the chr info:
-bcftools query -f '%CHROM\n' filename.vcf
-/
 *now, print out the chr\tpos
 bcftools query -f '%CHROM\t%POS\n' filename.vcf
 /

diff --git a/BCFtools cheat sheet b/BCFtools cheat sheet
@@ -161,3 +161,5 @@ bcftools view -H -i'GRCH37_38_REF_STRING_MATCH=1' ALL.chr7_GRCh38.genotypes.2017
 #And the contrary by doing:
 bcftools view -H -i'GRCH37_38_REF_STRING_MATCH=0' ALL.chr7_GRCh38.genotypes.20170504.ensembl.vcf.NA12878.biallelic.nonvariants.nonvalid.snps.vcf.gz |less
 /
+# Filtering a VCF depending on a certain Allele frequency:
+bcftools view -i 'INFO/AF > 0.8' z.vcf.gz
diff --git a/BCFtools cheat sheet b/BCFtools cheat sheet
@@ -17,9 +17,10 @@ bcftools view -r chr20:1-200000 -s NA20818,NA20819 filename.vcf.gz
 *print all variants except for the ones falling within region:
 bcftools view -t ^chr20:1-30000000 ex_bams.samtools.20161231.vcf.gz >out.vcf
 
-*view the positions passed in a file:
+*view the positions passed in a file (accepted files are .vcf and .bed):
 bcftools view -R 0002.vcf in.vcf.gz
 
+
 *view the positions passed in a tsv file:
 bcftools view -R 0002.tsv in.vcf.gz
 # The format of 0002.tsv:

diff --git a/BCFtools cheat sheet b/BCFtools cheat sheet
@@ -20,6 +20,12 @@ bcftools view -t ^chr20:1-30000000 ex_bams.samtools.20161231.vcf.gz >out.vcf
 *view the positions passed in a file:
 bcftools view -R 0002.vcf in.vcf.gz
 
+*view the positions passed in a tsv file:
+bcftools view -R 0002.tsv in.vcf.gz
+# The format of 0002.tsv:
+20      79000   80000
+20      90000   100000
+
 *printing out only the chr info:
 bcftools query -f '%CHROM\n' filename.vcf
 /

diff --git a/BCFtools cheat sheet b/BCFtools cheat sheet
@@ -153,3 +153,4 @@ bcftools view -H -i'GRCH37_38_REF_STRING_MATCH=1' ALL.chr7_GRCh38.genotypes.2017
 /
 #And the contrary by doing:
 bcftools view -H -i'GRCH37_38_REF_STRING_MATCH=0' ALL.chr7_GRCh38.genotypes.20170504.ensembl.vcf.NA12878.biallelic.nonvariants.nonvalid.snps.vcf.gz |less
+/
diff --git a/BCFtools cheat sheet b/BCFtools cheat sheet
@@ -141,3 +141,15 @@ bcftools view -u in.vcf.gz -o missing_genotypes.vcf.gz -Oz
 //
 #select a particular genotype (0/1 or 1/1) from a vcf. In this case access sample accessed by index 8:
 bcftools view -H combined.snps_indels_chr1.filt.vcf.gz.onlyvariants.vcf.gz.ensembl.vcf.gz.85706.vcf.gz -i 'GT[8]="het"'
+//
+#select all lines having exactly AC=2
+bcftools view -i'AC=2' in.vcf.gz
+//
+# if we have a tab in a VCF defined in the header like:
+##INFO=<ID=GRCH37_38_REF_STRING_MATCH,Number=0,Type=Flag,Description="Indicates reference allele in origin GRCh37 vcf string-matches reference allele in dbsnp GRCh38 vcf">
+/
+#we can check for the records having this tag by doing:
+bcftools view -H -i'GRCH37_38_REF_STRING_MATCH=1' ALL.chr7_GRCh38.genotypes.20170504.ensembl.vcf.NA12878.biallelic.nonvariants.nonvalid.snps.vcf.gz |less
+/
+#And the contrary by doing:
+bcftools view -H -i'GRCH37_38_REF_STRING_MATCH=0' ALL.chr7_GRCh38.genotypes.20170504.ensembl.vcf.NA12878.biallelic.nonvariants.nonvalid.snps.vcf.gz |less
diff --git a/BCFtools cheat sheet b/BCFtools cheat sheet
@@ -82,6 +82,9 @@ bcftools view -m3 -v snps input.vcf.gz
 #printing the set info in the INFO field:
 bcftools view -i 'set="freebayes_lcex"' combined.all.chr20.vcf.gz
 /
+#printing all entries having a quality <10
+bcftools view -i 'QUAL<10' in.vcf.gz
+/
 #removing FORMAT column from the VCF
 #it will remove all FORMAT annotations except the GT information
 bcftools annotate -x FORMAT ifile.vcf.gz

diff --git a/BCFtools cheat sheet b/BCFtools cheat sheet
@@ -50,6 +50,9 @@ bcftools query -l test.vcf
 *selecting the variants from a VCF (excluding 0|0 genotypes)
 bcftools view -c1 input.vcf
 /
+*selecting the non-variants from a VCF(AC=0)
+bcftools view -H -C0 concat.allchrs.sites.vcf.gz 
+/
 #filtering:
 /
 #using one of the INFO annotations (IDV)

diff --git a/BCFtools cheat sheet b/BCFtools cheat sheet
@@ -132,3 +132,6 @@ chr20   60280   .       TTTCCA  T       744     PASS    .
 //
 #selecting the missing (uncalled) genotypes:
 bcftools view -u in.vcf.gz -o missing_genotypes.vcf.gz -Oz
+//
+#select a particular genotype (0/1 or 1/1) from a vcf. In this case access sample accessed by index 8:
+bcftools view -H combined.snps_indels_chr1.filt.vcf.gz.onlyvariants.vcf.gz.ensembl.vcf.gz.85706.vcf.gz -i 'GT[8]="het"'
diff --git a/gistfile1.txt → BCFtools cheat sheet b/gistfile1.txt → BCFtools cheat sheet
diff --git a/gistfile1.txt b/gistfile1.txt
@@ -0,0 +1,134 @@
+*bcftools filter
+*Filter variants per region (in this example, print out only variants mapped to chr1 and chr2)
+qbcftools filter -r1,2 ALL.chip.omni_broad_sanger_combined.20140818.snps.genotypes.hg38.vcf.gz
+
+*printing out info for only 2 samples:
+bcftools view -s NA20818,NA20819 filename.vcf.gz
+
+*printing stats only for variants passing the filter:
+bcftools view -f PASS filename.vcf.gz
+
+*printing variants withoud header:
+bcftools view -H
+
+*printing variants on a particular region:
+bcftools view -r chr20:1-200000 -s NA20818,NA20819 filename.vcf.gz
+
+*print all variants except for the ones falling within region:
+bcftools view -t ^chr20:1-30000000 ex_bams.samtools.20161231.vcf.gz >out.vcf
+
+*view the positions passed in a file:
+bcftools view -R 0002.vcf in.vcf.gz
+
+*printing out only the chr info:
+bcftools query -f '%CHROM\n' filename.vcf
+/
+*now, print out the chr\tpos
+bcftools query -f '%CHROM\t%POS\n' filename.vcf
+/
+*now, print out the AF INFO field
+bcftools query -f '%INFO/AF\n'
+/
+#getting a particular annotation from the VCF
+bcftools query -f '%QUAL\n' 0002.vcf
+/
+#printing chr pos and a particular annotation from a VCF:
+bcftools query -f '%CHROM\t%POS\t%INFO/DP\n' in.vcf.gz
+/
+#printing out the sets assigned by GATK CombineVariants
+~/bin/bcftools-1.6/bcftools query -f '%set\n' out_combine.vcf.gz |sort |uniq
+/
+0#printing a list of samples from a VCF:
+bcftools query -l test.vcf
+/
+#also, the FORMAT annotations can be obtained by:
+~/bin/bcftools/bcftools query -f '[%GT]\n' ../0002.vcf |wc -l #the GT in this case
+/
+*selecting snps from file:
+~/bin/bcftools/bcftools view -v snps lc_bams.bcftools.20170319.NA12878.vcf.gz 
+/
+*selecting the variants from a VCF (excluding 0|0 genotypes)
+bcftools view -c1 input.vcf
+/
+#filtering:
+/
+#using one of the INFO annotations (IDV)
+bcftools filter -sFilterName -e'IDV<5' input.vcf
+/
+#OR logical operator:
+bcftools filter -sFilterName -e'DP>50000 | IDV<9' input.vcf
+/
+#filtering on FORMAT annotation:
+bcftools filter -sFilterName -e'FORMAT/DP<5' input.vcf
+/
+#filtering on INFO annotation:
+bcftools filter -sFilterName -e'INFO/DP<5' input.vcf
+/
+#printing out variants that pass the filter:
+~/bin/bcftools/bcftools view -f.,PASS lc_bams.bcftools.20170411.exc.norm.SNP.filtered.vcf.gz
+/
+#bcftools stats and filtering:
+~/bin/bcftools/bcftools stats -f "PASS,." file.vcf
+/
+#select only biallelic (excluding multiallelic) snps
+bcftools view -m2 -M2 -v snps input.vcf.gz
+/
+#select only the multiallelic snps
+bcftools view -m3 -v snps input.vcf.gz
+/
+#printing the set info in the INFO field:
+bcftools view -i 'set="freebayes_lcex"' combined.all.chr20.vcf.gz
+/
+#removing FORMAT column from the VCF
+#it will remove all FORMAT annotations except the GT information
+bcftools annotate -x FORMAT ifile.vcf.gz
+/
+#removing INFO field from VCF
+bcftools annotate --remove INFO in.vcf.gz
+/
+#annotating a vcf file using the annotations from a different VCF (in this case we only annotate the INFO/DP)
+bcftools annotate -c 'INFO/DP' -a annt.vcf.gz in.vcf.gz
+/
+#annotating a vcf file with a tabular file:
+see page https://github.com/samtools/bcftools/wiki/HOWTOs#annotate-from-bed
+/
+#drop individual genotype information
+bcftools view -G input.vcf.gz
+/
+#getting stats on the number of REF/ALT swaps and other things:
+bcftools +fixref file.bcf -- -f ref.fa
+/
+#correcting the REF/ALT swaps:
+bcftools norm --check-ref ws -f ref.fa in.vcf.gz -o out.vcf.gz -Oz
+//
+#changing the sample names in a VCF:
+#the samplenames.txt file has the following format:
+#oldsamplename newsamplename
+bcftools reheader -s samplenames.txt NA12878.giab.SNP.chr20.non_valid.vcf.gz -o NA12878.giab.SNP.chr20.non_valid.reheaded.vcf.gz
+//
+#changing the header:
+bcftools reheader -h newheader.txt ../combined.all.chr20.vcf.gz.snps.biallelic.vcf_chr20.vcf.gz.ensembl.vcf.gz.phased.ligated.NA12878.ucsc.vcf.gz -o combined.all.chr20.vcf.gz.snps.biallelic.vcf_chr20.vcf.gz.ensembl.vcf.gz.phased.ligated.NA12878.ucsc.reheaded.vcf.gz
+//
+# in order to use the plugins:
+export BCFTOOLS_PLUGINS=~/bin/bcftools-1.6/plugins/
+//
+# taqg2tag:
+# convert PL to GL
+bcftools +tag2tag in.vcf -- -r --pl-to-gl
+//
+# normalizing the multiallelic variants:
+
+# with -any I will split the multiallelic variants (SNPs+INDELs) into several records
+bcftools norm -m -any in.vcf.gz -o out.norm.vcf.gz -Oz
+
+For example:
+
+chr20   60280   .       TTTCCA  TTTCCATTCCA,T   744     PASS    .
+
+Will be converted to:
+
+chr20   60280   .       TTTCCA  TTTCCATTCCA     744     PASS    .
+chr20   60280   .       TTTCCA  T       744     PASS    .
+//
+#selecting the missing (uncalled) genotypes:
+bcftools view -u in.vcf.gz -o missing_genotypes.vcf.gz -Oz