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Mutect2 Amplicon realigment behavior

EADGEADG KielMember ✭✭✭

Hi there,

i was playing around with mutect2 and amplicons. I follow the best practise and run mutect2 with the following commands:

$java7Path\java -Xmx4g -jar $gatkPath\
-T MuTect2 \
-R $referencePath \
-I:tumor $I \
--dbsnp $dbSNP\
--cosmic $cosmic\
--artifact_detection_mode\
-bamout $bamOut\
-dt NONE \
-o $o

When i view the results a noticed that a evident call from the UG was missing in the mutect output. After i saw the bamOut from mutect, I release why... after the realignment all reads from the position were removed.

Here a view of both bam in igv:

Greetings EADG

Best Answer

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    I'm sorry, is this a question or just an observation? This is expected behavior, as documented for HaplotypeCaller. Realignment within the caller allows elucidation of such regions where the mapper makes mistakes.

  • EADGEADG KielMember ✭✭✭

    A mashup of both ;) I was digging a little bit deeper into the HC-Doc..i assume the bottom of the picture "shows" the active region for my sample. Is the determination of the active region influenced by the number of Reads ? So that regions with higher read counts had a better chance to get marked as active region ?

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Ah, got it. No, the active region triggering does not rely directly on the number of reads present; it's more a question of the proportion of reads showing non-reference bases. We don't want to be biased against low-coverage regions.

  • EADGEADG KielMember ✭✭✭

    Sry for my late reponse, i was on vacation:)

    @Geraldine_VdAuwera said:
    Ah, got it. No, the active region triggering does not rely directly on the number of reads present; it's more a question of the proportion of reads showing non-reference bases.

    Ok, do I interpret correctly that the start of my reads are to "blurry" to be recognized as active region.

    Thanks a lot.

    Greetings EADG

  • EADGEADG KielMember ✭✭✭

    Ty for the quick response...i used the "color by sample" option in IGV. I attach a screenshot showing the actual reads from the bamout.
    Can you anything more to it ;) ?

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