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!

Powered by Vanilla. Made with Bootstrap.
GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.
Register now for the upcoming GATK Best Practices workshop, Feb 20-22 in Leuven, Belgium. Open to all comers! More info and signup at

Fail retreiving variant calling, problem related with MappingQuality ?

mandormandor Member Posts: 8
edited January 2013 in Ask the GATK team

Dear all,

I fail retrieving variant calling (.vcf ) using the GATK2.0, although with a similar example it works well. I compared both and I find a difference in Mapping Quality (the mapping quality of the example that works has 60 whereas the other has 255 -this last one is performed using bfast and gives this quality-)

Googling, I already find that this could be caused because of GATK doesn't take into account qualities of 255. Is it true?
(Note than this solution affects to GATK1.4 and I am using the GATK2.0)

I also checked the reference genome was ok (and also the .bed file with the exom position).

I repeat the process changing manually the "255" to "60" with the same result.

Any ideas of what could be the problem?

The executed command :

java -jar /home/public/biotools/GATK_2.0/GenomeAnalysisTK.jar -T UnifiedGenotyper -R /home/public/mnt/cubix/public/biodata/hg19_norm/hg19.fa -L /home/public/mnt/cubix/public/biodata/hg19_norm/bed/all_captured_exomes_hg19.bed -I /home/public/test/outer_test/intermediate/AUT143_chr15_extract_cpy_sorted.bam -glm SNP -nt 4 -o /home/public/test/outer_test/intermediate/AUT143_chr15_extract_cpy_sorted.bam.vcf

$ samtools view AUT143_chr15_extract_cpy_sorted.bam | head
1629_189_1658_F3 0 15 20002423 255 2I48M * 0 0 TATCCAAATATCCACTTGCAGATTCCACGAAAATAGTGTTTCAAAACTGC 5:=59B98@>!!4<8C?72!!!!92::!!1373!!00!!-00!!.!!!!% XA:i:2 MD:Z:48 XE:Z:-----------3--------300-----1-----2---2----1--0-0- PG:Z:bfast RG:Z:sample IH:i:1 NH:i:1 HI:i:1 CM:i:10 NM:i:2 CQ:Z:!7B90A;/:A@<%>.>?5'.:?7>+/=)9'&22%%%&%(%%1&/%(/%%% OQ:Z:ARZ`SR!!LUU

]E>!!!!RCUO!!6AM@!!44!!3?@!!6!!!!% AS:i:925    CS:Z:T03320100333301120131300020111200032211200211000203
1396_1160_190_F3    16  15  20006225    255 50M *   0   0   CTCAATCTAAAGATAGGTTCAACTCTCTGAGATGAGTGCACACATCACAA  !!!!!!6/206B1!!!!38!!!!!2535:D41426372@A?86!!!!!!!  XA:i:2  MD:Z:26G4T18    XE:Z:0-310--------2-3---2-00--------------------13-2-2- PG:Z:bfast  RG:Z:sample IH:i:1  NH:i:1  HI:i:1  CM:i:13 NM:i:2  CQ:Z:!'''1+5-1:<A5%4.+''%8@+%1))'?%,?%1&%8%<<-.018:-%)- OQ:Z:!!!!!!RJGDR
J!!!!?M!!!!!;C?9TF57;BKBC__TG!!!!!!! AS:i:475 CS:Z:T02121311111131122132221222200022013223220032201320
(I also try to change manually the 255 value in .sam file (and I added 60) with no values ...)


Post edited by Geraldine_VdAuwera on


  • ebanksebanks Broad InstituteMember, Administrator, Broadie, Moderator, Dev Posts: 698 admin

    Hi there,

    Yes, as mentioned in the documentation we filter out reads with MQ=255. It looks like you are using an older version of Bfast, so I'd suggest you update to the latest version of Bfast where this bug is fixed.

    Eric Banks, PhD -- Director, Data Sciences and Data Engineering, Broad Institute of Harvard and MIT

  • mandormandor Member Posts: 8

    Thanks for your answer. But well, I have not the original fasta files in this case, only the .BAMs.

    My first attempt to change this manually already failed.

  • mandormandor Member Posts: 8

    Maybe a better question could be like that : "Supposing that the coordinates of the reads in the .bam file are correct, and also I am referring to good genome reference, what could be the other things than make that GATK avoid to use this reads ? (for Variant Calling)"

  • mandormandor Member Posts: 8
    edited August 2012

    Sorry, It is my fault. In one of my tests, I played with a extraction of a .bam file (I catched a wrong interval of manually detected variant callings ... ).

    The problem was related to MapQ, and I fixed the original .bam file using GATK command : "-T PrintReads -rf ReassignMappingQuality -DMQ 60".

    As pointed @ebanks, the reads are filtered with MQ=255. Thanks for the help! :)

    Post edited by mandor on
  • mandormandor Member Posts: 8

    Can myself change this discussion from state "Question" to state "Answered" ? [sorry for the inconvenience]

Sign In or Register to comment.