Variant lost when interval expanded.

[wangshun1121]

GATK version: gatk-4.2.3

I have two bam files: Tumor.bam is cfDNA data, and Normal.bam were reads from white blood cells.

There's a variant C to G at chr7:116795782 (hg38), I can get this variant using following command:

gatk --java-options -Xmx4000m Mutect2  \
  -R /Homo_sapiens_assembly38.fasta \
  -I Tumor.bam \
  -I Normal.bam \
  -normal GA03009QX \
  -L chr7:116795653-116795791 \
  --interval-padding 100 \
  -O output.vcf

and I can get the variant I want in output.vcf

##fileformat=VCFv4.2
##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=AF,Number=A,Type=Float,Description="Allele fractions of alternate alleles in the tumor">
...
##filtering_status=Warning: unfiltered Mutect 2 calls.  Please run FilterMutectCalls to remove false positives.
##normal_sample=GA03009QX
##source=Mutect2
##tumor_sample=GA03009CF
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	GA03009CF	GA03009QX
chr7	116795782	.	C	G	.	.	AS_SB_TABLE=1157,1223|8,9;DP=2519;ECNT=1;MBQ=20,20;MFRL=169,173;MMQ=60,60;MPOS=30;NALOD=1.23;NLOD=4.82;POPAF=6.00;TLOD=20.23	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:2357,17:8.145e-03:2374:739,8:746,4:1570,12:1145,1212,8,90/0:23,0:0.056:23:5,0:11,0:16,0:12,11,0,0

Then, I add 4 exon regions next to the exon where my variant is in interval_list.bed:

chr7    116781986	116782097
chr7    116783302   116783469
chr7	116795653	116795791
chr7	116795885	116796124
chr7	129189150	129189482

and I use similar GATK command line:

gatk --java-options -Xmx4000m Mutect2  \
  -R /Homo_sapiens_assembly38.fasta \
  -I Tumor.bam \
  -I Normal.bam \
  -normal GA03009QX \
  -L interval_list.bed \
  --interval-padding 100 \
  -O output.vcf

and the variant I want at chr7:116795782 LOST:

##filtering_status=Warning: unfiltered Mutect 2 calls.  Please run FilterMutectCalls to remove false positives.
##normal_sample=GA03009QX
##source=Mutect2
##tumor_sample=GA03009CF
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	GA03009CF	GA03009QX
chr7	116781913	.	T	C	.	.	AS_SB_TABLE=0,0|368,162;DP=540;ECNT=1;MBQ=0,20;MFRL=0,179;MMQ=60,60;MPOS=21;NALOD=-1.163e+01;NLOD=-1.133e+01;POPAF=6.00;TLOD=1695.59	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:0,527:0.997:527:0,190:0,194:0,384:0,0,365,162	0/0:0,3:0.800:3:0,2:0,1:0,3:0,0,3,0

Two bam files are in my following bams.zip: bams.zip