werid EGFR variant report

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linouhao

• February 21, 2022 10:24
• Edited

Dear professor,
Thanks a lot.

use vardict:
These days I found three Close in position variants in EGFR, but these seems to only have 1 in igv, and the support reads and vaf has a big gap. can you help me; I do noit know wtether I should report the p.L747_A750delinsP as vaf 5.41% and whether I should report the three

 

use gatk : only get one variant

chr7    55242478    .    G    C    .    PASS    AS_FilterStatus=SITE;AS_SB_TABLE=82,68|22,30;DP=205;ECNT=2;GERMQ=93;MBQ=20,20;MFRL=190,208;MMQ=60,60;MPOS=32;POPAF=7.30;ROQ=93;TLOD=182.74    GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB    0|1:150,52:0.266:202:59,25:52,14:129,46:0|1:55242465_GGAATTAAGA_G:55242465:82,68,22,30

 

use mutscan:

EGFR-pos-7-55249071-20-c.2369C>T-p.T790M-COSM6240 TCTGCCTCACCTCCACCGTGCAGCTCATCA T GCAGCTCATGCCCTTCGGCTGCCTCCTGGA chr7
EGFR-pos-7-55242469:55242478-c.2239_2248TTAAGAGAAG>C(Complex)-p.L747_A750>P-COSM12382 AAAGTTAAAATTCCCGTCGCTATCAAGGAA C CAACATCTCCGAAAGCCAACAAGGAAATCC chr7

REQUIRED for all errors and issues:
a) GATK version used:

4.2.5.0
b) Exact command used:

$gatk Mutect2 -R $ref_fasta  -L $result_dir/$sample.bed  -I $result_dir/${sample}_gencore.bam  -germline-resource $af_only_gnomad_vcf --native-pair-hmm-threads 96 --f1r2-tar-gz $result_dir/$sample.f1r2.tar.gz  -O $result_dir/$sample.unfiltered.vcf

 
c) Entire program log:

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  linouhao

  • February 20, 2022 06:38

  this is a very important variant related to EGFR drug. So I am concerned about it. thanks a lot

  

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  Genevieve Brandt (she/her)

  • February 22, 2022 17:13

  Hi linouhao,

  I am going to move your post into our Community Discussions -> General Discussion topic, as the Somatic topic is for reporting bugs and issues with GATK.

  You can read more about our forum guidelines and the topics here: Forum Guidelines.

  Best,

  Genevieve

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  linouhao

  • February 23, 2022 00:06

  sorry for thatGenevieve Brandt (she/her)

  is there a link of that and can you have alook at my question

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  Genevieve Brandt (she/her)

  • February 23, 2022 01:54

  Here is the link for the General Discussion forum topic: https://gatk.broadinstitute.org/hc/en-us/community/topics/360002143692-General-Discussion

  And all the forum topics listed: https://gatk.broadinstitute.org/hc/en-us/community/topics

  We address questions in the order they are received. 

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  linouhao

  • February 23, 2022 01:58

  thanks a  lotGenevieve Brandt (she/her)

  hope you will have a look when free

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  linouhao

  • February 27, 2022 10:21

  thanks a  lotGenevieve Brandt (she/her)

   

  any response about this?

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  Genevieve Brandt (she/her)

  • March 09, 2022 23:10

  Hi linouhao,

  Thank you for your patience! We have had many questions on the forum recently. 

  Our support team can only provide support for GATK tools and questions, we don't have any insight into the vardict results. Is there anything about the GATK result you have a question about?

  Best,

  Genevieve

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  linouhao

  • March 09, 2022 23:15

  Thanks a lot   Genevieve Brandt (she/her)

  In the first question, I have talked about the result.

  use gatk : only get one variant

  chr7    55242478    .    G    C    .    PASS    AS_FilterStatus=SITE;AS_SB_TABLE=82,68|22,30;DP=205;ECNT=2;GERMQ=93;MBQ=20,20;MFRL=190,208;MMQ=60,60;MPOS=32;POPAF=7.30;ROQ=93;TLOD=182.74    GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB    0|1:150,52:0.266:202:59,25:52,14:129,46:0|1:55242465_GGAATTAAGA_G:55242465:82,68,22,30

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  Genevieve Brandt (she/her)

  • March 09, 2022 23:41

  linouhao you can force call sites of interest with the option --alleles. Then, you can see the evidence for these variants with GATK. Here is the explanation of this option in the tool docs: https://gatk.broadinstitute.org/hc/en-us/articles/4418062771227-Mutect2#--alleles

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  linouhao

  • March 10, 2022 00:00

  thanks a lotGenevieve Brandt (she/her)

  yeah, it maybe a method. 

  but it is clear in igv, I want to know why gatk ignore it, it is a hot point, would you like to have a look at bam file, I can send it to you

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  Genevieve Brandt (she/her)

  • March 10, 2022 00:21

  We have an article that might be helpful for why variants of interest are not called sometimes: https://gatk.broadinstitute.org/hc/en-us/articles/360043491652-When-HaplotypeCaller-and-Mutect2-do-not-call-an-expected-variant

  Could you share the variant records when you force call these sites?

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  linouhao

  • March 10, 2022 00:28

  thanks a lotGenevieve Brandt (she/her)

  I alsohave read that, but still can not get the reason

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  Genevieve Brandt (she/her)

  • March 10, 2022 00:45

  I see! Can you share the variant records when you force call these sites?

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