Question: samtools mpileup to bcftools mpileup
2
gravatar for Ric
7 months ago by
Ric240
Australia
Ric240 wrote:

I got

samtools mpileup option `u` is functional, but deprecated. Please switch to using bcftools mpileup in future.

How could I convert the following commands to bcftools mpileup ?

samtools mpileup -uf QMg-NbQ3P-RN.fasta aln_P1O1.sorted.bam | bcftools view -bvcg - > P1O1_var.raw.bcf
bcftools view P1O1_var.raw.bcf | vcfutils.pl varFilter -D100 > P1O1_var.flt.vcf

Thank you in advance.

snp samtools bcftools • 829 views
ADD COMMENTlink modified 7 months ago by zx87547.5k • written 7 months ago by Ric240
1
gravatar for finswimmer
7 months ago by
finswimmer11k
Germany
finswimmer11k wrote:

Hello Ric ,

first make sure you have the latest version of samtools and bcftools.

$ bcftools mpileup -Ou QMg-NbQ3P-RN.fasta aln_P1O1.sorted.bam | bcftools call -Ou -mv  | bcftools norm -Ou -f QMg-NbQ3P-RN.fasta | bcftools view -e 'FORMAT/DP > 100' > P1O1_var.flt.vcf
  • The bcftools view command you showed was only used for bcftools version < 1 and is replaced by bcftools call
  • I recommend to normalize your indel variants, that's why I added a bcftools norm step
  • For removing variants with read depth greater 100 I used bcftools view

fin swimmer

ADD COMMENTlink written 7 months ago by finswimmer11k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1981 users visited in the last hour