Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

After using Gatk for realignment + recalibration, then samtools for calling : what step is missing ?

Christine31Christine31 Member
edited January 2013 in Ask the GATK team

Hello,

I am new at using GATK (v 2.1-3). I do exome sequencing by sample using the following steps:
Alignment with BWA (0.6.2)
GATK :Local realignment around INDELs
PICARD (1.67): FixMateInformation
GATK: Recalibration (BaseRecalibrator + PrintReads -BQSR)
Samtools for calling variants

Samtools seems to run properly but no file (*.vcf and *.bcf) are created and no error message is prompted :

cd Sample_09

  • samtools mpileup -BE -ug -q 20 -Q 20 -D -f human_g1k_v37.fasta realigned_fixed_recal.bam -C50
  • bcftools view -bvcg -
    [mpileup] 1 samples in 1 input files
    Set max per-file depth to 8000
    [bcfview] 100000 sites processed.
    [afs] 0:89274.054 1:6411.053 2:4314.893
    [bcfview] 200000 sites processed.
    [afs] 0:89100.642 1:6125.883 2:4773.474
    [bcfview] 300000 sites processed.
    [afs] 0:87374.996 1:7439.238 2:5185.766
    [bcfview] 400000 sites processed.
    [afs] 0:87890.186 1:7087.628 2:5022.185
    [bcfview] 500000 sites processed.
    [afs] 0:85322.061 1:8454.843 2:6223.096
    [bcfview] 600000 sites processed.
    [afs] 0:85864.368 1:8410.777 2:5724.854
    [bcfview] 700000 sites processed.
    [afs] 0:88813.814 1:6828.001 2:4358.185
    [bcfview] 800000 sites processed.
    [afs] 0:89070.318 1:6302.924 2:4626.758
    [bcfview] 900000 sites processed.
    [afs] 0:88364.380 1:6796.962 2:4838.658
    [bcfview] 1000000 sites processed.
    [afs] 0:86892.531 1:7268.088 2:5839.381
    [bcfview] 1100000 sites processed.
    [afs] 0:87184.845 1:7153.073 2:5662.081
    [bcfview] 1200000 sites processed.
    [afs] 0:86762.756 1:7241.236 2:5996.008
    [bcfview] 1300000 sites processed.
    [afs] 0:89346.143 1:6159.989 2:4493.868
    [bcfview] 1400000 sites processed.
    [afs] 0:88658.355 1:7160.555 2:4181.089
    [bcfview] 1500000 sites processed.
    [afs] 0:85985.305 1:8308.039 2:5706.656
    [bcfview] 1600000 sites processed.
    [afs] 0:87346.636 1:7708.883 2:4944.480
    [afs] 0:63097.202 1:3950.127 2:3572.670

  • bcftools view .bcf

+ cd ..

I have seen that some groups use after realignment Picard:AddOrReplaceReadGroups and I wonder if I should use before calling the variant with samtools.

Thanks in advance for any advice you can give me.

Chris

Post edited by Geraldine_VdAuwera on

Best Answer

Answers

Sign In or Register to comment.