The current GATK version is 3.7-0
Examples: Monday, today, last week, Mar 26, 3/26/04

Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

Get notifications!

You can opt in to receive email notifications, for example when your questions get answered or when there are new announcements, by following the instructions given here.

Did you remember to?

1. Search using the upper-right search box, e.g. using the error message.
2. Try the latest version of tools.
3. Include tool and Java versions.
4. Tell us whether you are following GATK Best Practices.
5. Include relevant details, e.g. platform, DNA- or RNA-Seq, WES (+capture kit) or WGS (PCR-free or PCR+), paired- or single-end, read length, expected average coverage, somatic data, etc.
6. For tool errors, include the error stacktrace as well as the exact command.
7. For format issues, include the result of running ValidateSamFile for BAMs or ValidateVariants for VCFs.
8. For weird results, include an illustrative example, e.g. attach IGV screenshots according to Article#5484.
9. For a seeming variant that is uncalled, include results of following Article#1235.

Did we ask for a bug report?

Then follow instructions in Article#1894.

Formatting tip!

Wrap blocks of code, error messages and BAM/VCF snippets--especially content with hashes (#)--with lines with three backticks ( ``` ) each to make a code block as demonstrated here.

Jump to another community
Picard 2.9.0 is now available. Download and read release notes here.
GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.

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

Christine31Christine31 Posts: 2
edited January 2013 in Ask the GATK team


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.


Post edited by Geraldine_VdAuwera on

Best Answer

  • Mark_DePristoMark_DePristo Broad InstitutePosts: 153 admin
    Accepted Answer

    Hi Christine31, you should contact the samtools mailing list for help with that tool.

    Mark A. DePristo, Ph.D.
    Co-Director, Medical and Population Genetics
    Broad Institute of MIT and Harvard


Sign In or Register to comment.