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Variant called if HC is run on individual bam but variant not called on multiple input bam

ZakiZaki Posts: 4Member
edited February 25 in Ask the GATK team

Dear Team,

I encounter a situation when ;

If I run Haplotype caller on one .bam file - Haplotype caller called the mutation (sanger validated)

java GenomeAnalysisTK.jar -T HaplotypeCaller -nct 15 -minPruning 2 \
-R genome.fa  \
-I sample_1.bam   \
-L TP53.bed \
-U ALLOW_N_CIGAR_READS \
-o sample_1.vcf

But, If i run Haplotype caller with multiple bam as input - Haplotype caller failed to call the mutation in the sample mentioned above

java GenomeAnalysisTK.jar -T HaplotypeCaller -nct 15 -minPruning 2 \
-R genome.fa  \
-I sample_1.bam   -I sample_2.bam -I sample_3 .bam ..... -I sample_19.bam \
-L TP53.bed \
-U ALLOW_N_CIGAR_READS \
-o multisample.vcf

I used the -bamOutput option to view the .bam file HC would expect to see when calling the mutation. Please find below IGV screenshot

java GenomeAnalysisTK.jar -T HaplotypeCaller -nct 15 -minPruning 2 \
-R genome.fa  \
-I sample_1.bam   -I sample_2.bam -I sample_3 .bam ..... -I sample_19.bam \
-L TP53.bed \
-U ALLOW_N_CIGAR_READS \
--bamOutput multiple_all.bam --bamWriterType ALL_POSSIBLE_HAPLOTYPES \
-o multisample.vcf

1st row is HC run only on sample_1.bam
2nd row is HC run on multiple.bam input - using the --bamOutput option alone
3rd row is HC run on multiple.bam input - using the --bamOutput option + --bamWriterType ALL_POSSIBLE_HAPLOTYPES

The coverage on the 1st row (IGV) of sample1 is 262 (Ref(C):3, Mut(A):259)
The coverage on the 3rd row (IGV) file at the position of interest is 3627(Ref(C):3411, Mut(A):215, G:1 , DEL:13)

Could the reason why HC unable to call the mutation (when multiple.bam are used as input) is because the postion of interest is has too much noise ~3 base upstream? (shown in screen shot below)

Any help understanding why mulisample bam input would fail to call the variant would me most helpful.

Thanks in advance

Post edited by Zaki on

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