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• Calling heterozygous and homozygous SNPs with SAMtools or VCF ?
  When calling SNPs with samtools, I need to know which one is Hetero or Homozygote. I tried the f...
• Why Do We Need To Set Maximal Read Depth In Samtools
  I analyse reads from Ion Torrent platform with bwa-samtools pipeline. I used them in such way: b...
• Failed to open var.raw.bcf: unknown file type
  Hi, I used the following commands to call SNPs samtools merge ${1}/all.sorted.dedup.bam ${1}...
• How Do You Get The Quality Score And Coverage For Every Single Position Of A Reference Assembly
  Hi, I am trying to extract the coverage and the average quality score for each position of a ref...
• Variant calling using samtools
  I have cancer dataset containing 10 tumor and 10 control pairs. Each tumor or control dataset is ...
• BCFtools outputs error : [bcf_sync] incorrect number of fields (6 != 5)
  I launched samtools to call SNPs on 2 BAM files, and when it comes to BCFtools, both returned an ...
• How To Interpret -D File In Samtools Variant Calling Pipeline?
  I have been using using the samtools pipeline for variant calling for a while now and have just m...
• samtools mpileup to bcftools mpileup
  I got samtools mpileup option `u` is functional, but deprecated. Please switch to using bc...
• Bcftools Mpileup Removes Marked Duplicates?
  Hey, My question is does samtools mpileup automatically removed duplicates from test.marked.bam ...
• Error in bcftools view -bvcg command
  I am using this pipeline to make a vcf file. but m having problem at step 4. `bcftools view -bvcg...
• Which Parameters Are You Using For Samtools Mpileup And Bcftools To Compare Human Cells To See Individual Differences?
  Which parameters are you using for samtools mpileup and bcftools to compare human cells to see in...
• How To Filter The Snps/Indel Results From Mpileup?
  Hi. I trid to use mpileup to identified the SNP/Indels. The commands I used were: samtools fillm...
• Mpileup -D And -S
  I am calling out SNPs from a high coverage (> 20fold) 75bp paired-end, > 400 million reads ...
• Interpreting Results From Mpileup
  Hi! I am stuck with concluding a variant call I made on two BAM files (two samples). Say sample...
• Variant Calling (Samtools Mpileup): Error
  Hi, I am trying to update a variant calling script came from the predecessors. I am getting the ...
• Samtools Mpileup Snp Calling Improperly Paired Reads
  I'm doing samtools mpileup snp calling but samtools is not including reads that are improperly pa...
• Using vcfutils.pl command
  I am trying to do some variant filtering via samtools and have made a var.bcf file.  When I try ...
• Reducing sequencing errors in .vcf file
  I am trying different things in Samtools to get a reasonable .vcf file for 2 human exomes I have ...