I'm confused by your statement that the 'END' position isn't taken into account? The first variant at 5:50 starts before your range and is included because it overlaps into your defined region?
Hello, Thank you for the very practical tutorial on bcftools. I have a question if you don't mind. I want to filter my VCF file (my VCF file just contains SNPs) to remove homozygous variants. I have done the annotation on the file as well. so now my question is that for filtering the homozygous variants with bcftools should I use the annotated VCF file or the one without annotation? Thank you very much.
You are lifesaver!! Thank you from Czech Republic :) .
I have found myself returning to this video tens of times. Appreciate your hard work!
Offspring guitarist has a PhD in biology which is awesome too. Great band name for genetics
thank you very much
Holy shit this is great, you've just inspired me to use the less command
Looking to annotate a SAM file with the BED file. Can I use
$ bcftools annotate -a sample.bed -s sample.sam -c CHROM,POS,REF,ALT,-,TAG file.vcf
Great video, thanks. can you using snv file to make a video about norm or other functions of bcftools, please.
I'm confused by your statement that the 'END' position isn't taken into account? The first variant at 5:50 starts before your range and is included because it overlaps into your defined region?
This is great. How can I rename INFO subtags like INFO/RD2 into INFO/INFO?
Can you please tell me the command to extract variants where sample1 is 0/0 when sample2 is 1/1 and sample1 is 1/1 when sample2 is 0/0
Hello, Thank you for the very practical tutorial on bcftools. I have a question if you don't mind. I want to filter my VCF file (my VCF file just contains SNPs) to remove homozygous variants. I have done the annotation on the file as well. so now my question is that for filtering the homozygous variants with bcftools should I use the annotated VCF file or the one without annotation?
Thank you very much.