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Bcftools mpileup

1

I am using 91 bam files each of 500 mb size Bam files sorted and indexed and reference maize genome is also indexed of 2.5 gb . Then i proceeded...

Mashindersingh

[mpileup2] How does mpileup choose the reads for later calling, and is the -d flag behaving strangely?

1

Hi bcftools team, I have a conceptual question about mpileup and I think the -d flag is either being weird or I'm misunderstanding how it works. I am using bcftools...

goeckeritz

Add --verbosity flag like samtools

1

I've been using bcftools with Google Cloud Storage support, and it would be very useful to be able to pass verbosity into htslib in order to understand how the http...

pettyalex

Merge adjacent sites into a complex

1

17 37880996 . T TTTA . PASS AS_FilterStatus=SITE;AS_SB_TABLE=2337,1597|178,137;DP=4390;ECNT=2;GERMQ=93;MBQ=35,36;MFRL=184,191;MMQ=60,60;MPOS=26;NALOD=2.09;NLOD=506.28;POPAF=6.00;TLOD=1053.35 17 37880997 . G T . PASS AS_FilterStatus=SITE;AS_SB_TABLE=2337,1597|178,137;DP=4408;ECNT=2;GERMQ=93;MBQ=35,34;MFRL=184,191;MMQ=60,60;MPOS=26;NALOD=2.09;NLOD=506.29;POPAF=6.00;TLOD=1053.34 These two sites are close to each other and should be merged into the...

xfk274280

How to format a file to extract a set of SNPs from a BCF file?

5

Hello, in order to run: bcftools view -T mylist.txt file.bcf -Ou -o filteredfile.bcf can you please show me how a first few lines of "mylist.txt" should look like? Thanks Ana

montenegrina

How does bcftools isec identify the same sites

1

I used bcftools isec to find common sites in multiple vcf files. But I found a confused site. The records from vcfs are: >>> vcf1 chr3 183987815 . G A...

ym-chen