I have noticed a strange behavior of GATK Mutect2, especially the variant 13-33329989-TGTCTC-T is called if the BED file used in the command contains:

13  33329959    33330170

and is not called if another BED is used that contains:

13  33329974    33330100

but BOTH of them contain the 33329989 position.

Does anybody have a clue of why I'm getting this??

Here the results and LOG of both commands:

Here the result of the first command (13:33329959-33330170):

awk -F'\t' '$1 == 13' /home/ec3408/prove/prova.GHARCKDI16uuC14501.chr13_33329959_33330170.vcf

13  33329962    .   G   T   .   .   DP=71;ECNT=7;MBQ=31,11;MFRL=237,311;MMQ=60,60;MPOS=25;POPAF=2.82;TLOD=7.45  GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:66,5:0.069:71:33,0:18,1:0|1:33329962_G_T:33329962:49,17,4,1
13  33329971    .   C   T   .   .   DP=86;ECNT=7;MBQ=30,14;MFRL=221,299;MMQ=60,60;MPOS=19;POPAF=3.10;TLOD=19.07 GT:AD:AF:DP:F1R2:F2R1:SB    0/1:73,10:0.123:83:32,0:24,3:49,24,9,1
13  33329976    .   TCAGAAAAA   T   .   .   DP=109;ECNT=7;MBQ=32,33;MFRL=226,418;MMQ=60,60;MPOS=11;POPAF=7.30;TLOD=3.76 GT:AD:AF:DP:F1R2:F2R1:SB    0/1:106,3:0.034:109:49,0:37,3:73,33,2,1
13  33329987    .   A   T   .   .   DP=112;ECNT=7;MBQ=31,21;MFRL=225,283;MMQ=60,60;MPOS=-1073741822;POPAF=7.30;TLOD=7.93    GT:AD:AF:DP:F1R2:F2R1:SB    0/1:106,5:0.052:111:45,0:41,2:70,36,4,1
13  33329989    .   TGTCTC  T   .   .   DP=120;ECNT=7;MBQ=32,27;MFRL=223,279;MMQ=60,60;MPOS=-2147483648;POPAF=7.30;TLOD=3.66    GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:117,3:0.031:120:56,1:48,1:0|1:33329962_G_T:33329962:74,43,2,1
13  33329996    .   TCTACCAGAG  T   .   .   DP=129;ECNT=7;MBQ=32,25;MFRL=223,279;MMQ=60,60;MPOS=-2147483648;POPAF=7.30;TLOD=3.54    GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:126,3:0.029:129:62,0:48,2:0|1:33329962_G_T:33329962:75,51,2,1
13  33330007    .   A   T   .   .   DP=130;ECNT=7;MBQ=31,22;MFRL=222,279;MMQ=60,60;MPOS=-2147483648;POPAF=7.30;TLOD=3.53    GT:AD:AF:DP:F1R2:F2R1:SB    0/1:127,3:0.028:130:59,0:46,1:72,55,2,1

and here the LOG:

/nfs/goldstein/software/gatk-4.1.2.0/gatk \
>                 --java-options -Xmx11000m Mutect2 \
>                 -R /nfs/goldstein/goldsteinlab/somatic_calling/references/b37/hs37d5.fa \
>                 -I /nfs/igmdata01/ALIGNMENT/BUILD37/DRAGEN/EXOME/GHARCKDI16uuC14501.91405/GHARCKDI16uuC14501.91405.realn.recal.bam \
>                 -L regions/prova.chr13_33329959_33330170.bed \
>                 --germline-resource /nfs/goldstein/software/gatk-4.1.2.0/Mutect2/af-only-gnomad.raw.sites.b37.vcf.gz \
>                 --panel-of-normals /nfs/goldstein/goldsteinlab/somatic_calling/PON/PON-roche.vcf.gz \
>                 -O /home/ec3408/prove/prova.GHARCKDI16uuC14501.chr13_33329959_33330170.vcf

Here the result of the second command chr13:33329974-33330100

awk -F'\t' '$1 == 13' /home/ec3408/prove/prova.GHARCKDI16uuC14501.chr13_33329974_33330100.vcf

### empty ###

and here the LOG:

/nfs/goldstein/software/gatk-4.1.2.0/gatk \
>                 --java-options -Xmx11000m Mutect2 \
>                 -R /nfs/goldstein/goldsteinlab/somatic_calling/references/b37/hs37d5.fa \
>                 -I /nfs/igmdata01/ALIGNMENT/BUILD37/DRAGEN/EXOME/GHARCKDI16uuC14501.91405/GHARCKDI16uuC14501.91405.realn.recal.bam \
>                 -L regions/prova.chr13_33329974_33330100.bed \
>                 --germline-resource /nfs/goldstein/software/gatk-4.1.2.0/Mutect2/af-only-gnomad.raw.sites.b37.vcf.gz \
>                 --panel-of-normals /nfs/goldstein/goldsteinlab/somatic_calling/PON/PON-roche.vcf.gz \
>                 -O /home/ec3408/prove/prova.GHARCKDI16uuC14501.chr13_33329974_33330100.vcf