We are trying to retrieve a SNP that is present in the BAM file when using BWA-MEM. When looking at the bamout file we can see that there is a SNP (A->G), but when looking into the VCF file it gives a score of 0/0. Below is an IGV snippet with the amount of bases for the positions we expect a SNP. From top to bottom:
1: BAM file after mapping with BWA
2: GATK command: gatk HaplotypeCaller -R ref.fasta -ERC GVCF -bamout sample.basic.bam -I sample.sorted.bam -O sample.basic.gvcf
VCF file: BaseQRankSum=-1.399;DP=97;ExcessHet=3.0103;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=0.000;RAW_MQandDP=349200,97;ReadPosRankSum=0.000 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|0:83,6,0:89:46:0|1:100_A_G:0,46,1508,206,1525,1685:100:0,83,0,6
3: GATK command: gatk HaplotypeCaller -R ref.fasta -ERC GVCF -bamout sample.standard.bam --dont-use-soft-clipped-bases true --do-not-run-physical-phasing true -I sample.sorted.bam -O sample.standard.gvcf
VCF file: BaseQRankSum=-0.739;DP=90;ExcessHet=3.0103;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=0.000;RAW_MQandDP=324000,90;ReadPosRankSum=0.000 GT:AD:DP:GQ:PL:SB 0/0:77,5,0:82:42:0,42,1432,190,1447,1595:0,77,0,5
4:GATK command: gatk HaplotypeCaller -R ref.fasta -ERC GVCF --dont-use-soft-clipped-bases true --do-not-run-physical-phasing true -bamout sample.bruijn.bam --linked-de-bruijn-graph true -I sample.sorted.bam -O sample.bruijn.gvcf
VCF file: DP=37;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=133200,37 GT:AD:DP:GQ:PL:SB 0/1:33,4,0:37:46:46,0,1143,144,1155,1300:0,33,0,4
In the bottom track I also tried to use the --linked-de-bruijn-graph, but this does not give the results I expect.
version of GATK that I am using: v126.96.36.199
Is there another option that I missed that shows the reads under position 100 or is there another explanation?
Thanks in advance.
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