Hey,
I've been testing mPileup with parameters -B, -E, or neither, and I noticed something weird.
Neither:
chr1 165656243 G T 3.01 DP=12;VDB=0.0287;AF1=0.4997;AC1=1;DP4=6,2,3,0;MQ=60;FQ=4.77;PV4=1,1.7e-10,1,1
With -B:
chr1 165656243 G T 45 DP=12;VDB=0.0287;AF1=0.5;AC1=1;DP4=6,2,3,1;MQ=60;FQ=48;PV4=1,1,1,0.46
With -E:
chr1 165656243 G T 18.1 DP=12;VDB=0.0287;AF1=0.5;AC1=1;DP4=6,2,3,0;MQ=60;FQ=21;PV4=1,1,1,1
It gets the same call for all 3 with different quality scores. However, the weird part is that when looking at this in IGV, or with GATK DepthOfCoverage, there are 17 reads that covers this spot, not just 12. 12 reads are G and 5 reads are T (by IGV). All of the reads have a mapping quality of 150 except one has a mapping quality of 82. All of the bases have a Phred quality score of 29 or greater. My commands (after aligning/sorting/de-duping/sorting/realigning around indels/sorting) were (3 separate for -E, -B, or neither):
samtools-0.1.18/samtools mpileup -E -ugf hg18_reference_seq.fa aligned_file.bam | /samtools-0.1.18/bcftools/bcftools view -bvcg -> Intermediate_File
samtools-0.1.18/bcftools/bcftools view Intermediate_File | samtools-0.1.18/bcftools/vcfutils.pl varFilter -D99999 > called_variants
Anybody have any ideas?
I've been testing mPileup with parameters -B, -E, or neither, and I noticed something weird.
Neither:
chr1 165656243 G T 3.01 DP=12;VDB=0.0287;AF1=0.4997;AC1=1;DP4=6,2,3,0;MQ=60;FQ=4.77;PV4=1,1.7e-10,1,1
With -B:
chr1 165656243 G T 45 DP=12;VDB=0.0287;AF1=0.5;AC1=1;DP4=6,2,3,1;MQ=60;FQ=48;PV4=1,1,1,0.46
With -E:
chr1 165656243 G T 18.1 DP=12;VDB=0.0287;AF1=0.5;AC1=1;DP4=6,2,3,0;MQ=60;FQ=21;PV4=1,1,1,1
It gets the same call for all 3 with different quality scores. However, the weird part is that when looking at this in IGV, or with GATK DepthOfCoverage, there are 17 reads that covers this spot, not just 12. 12 reads are G and 5 reads are T (by IGV). All of the reads have a mapping quality of 150 except one has a mapping quality of 82. All of the bases have a Phred quality score of 29 or greater. My commands (after aligning/sorting/de-duping/sorting/realigning around indels/sorting) were (3 separate for -E, -B, or neither):
samtools-0.1.18/samtools mpileup -E -ugf hg18_reference_seq.fa aligned_file.bam | /samtools-0.1.18/bcftools/bcftools view -bvcg -> Intermediate_File
samtools-0.1.18/bcftools/bcftools view Intermediate_File | samtools-0.1.18/bcftools/vcfutils.pl varFilter -D99999 > called_variants
Anybody have any ideas?
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