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differences in coverage BEDtools - samtools mpileup
Hi,
I have been using samtools mpileup and BEDtools coverageBed under default settings to count coverages at SNP sites identified with samtools mpileup. Both programs used the same paired BAM files produced by the Bioscope reference mapper as input. Samtools mpileup should report coverages under the DP and (quality checked) DP4 values in the vcf-fileoutput, while coverageBed reports all features in the file covering identified sites. I noted that BEDtools counts are much higher than those reported by samtools.
What am I getting wrong? Or if not, based on what criteria are reads counted? Any suggestions much appreciated!
samtools 0.1.16 (r963:234):
samtools mpileup -uf ref.fa aln1.bam aln2.bam | bcftools view -bvcg - > var.raw.bcf
bcftools view var.raw.bcf | vcfutils.pl varFilter -D100 > var.flt.vcf
coverageBed (v2.12.0):
samtools view -b /path/to/folder/A_paired_sorted.bam | ./coverageBed -abam /path/to/folder/A_paired_sorted.bam -b /path/to/folder/SNPs_zerobased.bed > /path/to/folder/counts_A_s.txt
fileformat SNPs_zerobased.bed file(includes only sites which interest me):
scaffold_1 7354 7355
example vcf line (4 separate samples sequenced):
scaffold_1 7355 . A T 257 . DP=15;AF1=0.8585;CI95=0.625,0.875;DP4=0,1,0,12;MQ=34;FQ=-7.6;PV4=1,0.34,0.058,0.41 GT:PL
P:SP:GQ 1/1:36,6,0:2:0:11 1/1:82,9,0:3:32668:13 0/1:81,0,28:4:8249856:24 1/1:101,12,0:4:0:16
separate counts in coverageBeds for each sample
scaffold_1 7354 7355 4 1 1 1.0000000
scaffold_1 7354 7355 5 1 1 1.0000000
scaffold_1 7354 7355 6 1 1 1.0000000
scaffold_1 7354 7355 6 1 1 1.0000000
counts from samtools mpileup: DP=15 (DP4=13)
counts from coverageBed: 21
I have been using samtools mpileup and BEDtools coverageBed under default settings to count coverages at SNP sites identified with samtools mpileup. Both programs used the same paired BAM files produced by the Bioscope reference mapper as input. Samtools mpileup should report coverages under the DP and (quality checked) DP4 values in the vcf-fileoutput, while coverageBed reports all features in the file covering identified sites. I noted that BEDtools counts are much higher than those reported by samtools.
What am I getting wrong? Or if not, based on what criteria are reads counted? Any suggestions much appreciated!
samtools 0.1.16 (r963:234):
samtools mpileup -uf ref.fa aln1.bam aln2.bam | bcftools view -bvcg - > var.raw.bcf
bcftools view var.raw.bcf | vcfutils.pl varFilter -D100 > var.flt.vcf
coverageBed (v2.12.0):
samtools view -b /path/to/folder/A_paired_sorted.bam | ./coverageBed -abam /path/to/folder/A_paired_sorted.bam -b /path/to/folder/SNPs_zerobased.bed > /path/to/folder/counts_A_s.txt
fileformat SNPs_zerobased.bed file(includes only sites which interest me):
scaffold_1 7354 7355
example vcf line (4 separate samples sequenced):
scaffold_1 7355 . A T 257 . DP=15;AF1=0.8585;CI95=0.625,0.875;DP4=0,1,0,12;MQ=34;FQ=-7.6;PV4=1,0.34,0.058,0.41 GT:PL
P:SP:GQ 1/1:36,6,0:2:0:11 1/1:82,9,0:3:32668:13 0/1:81,0,28:4:8249856:24 1/1:101,12,0:4:0:16separate counts in coverageBeds for each sample
scaffold_1 7354 7355 4 1 1 1.0000000
scaffold_1 7354 7355 5 1 1 1.0000000
scaffold_1 7354 7355 6 1 1 1.0000000
scaffold_1 7354 7355 6 1 1 1.0000000
counts from samtools mpileup: DP=15 (DP4=13)
counts from coverageBed: 21
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