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Picard 2.10.4 has MAJOR CHANGES that impact throughput of pipelines. Default compression is now 1 instead of 5, and Picard now handles compressed data with the Intel Deflator/Inflator instead of JDK.
GATK version 4.beta.3 (i.e. the third beta release) is out. See the github release page for download and details.

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

Christine31Christine31 Member
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


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