I am getting different counts for the number of bases on reference covered by aligned reads.

Question

[Anop Singh Ranawat]

samtools mpileup

samtools mpileup -B -Q0 -d100000 sample_sort.bam -f hg19.fa | grep "32417945"

chr11 32417945 T 5671

===

samtools depth

samtools depth sample_sort.bam | grep "32417945"

chr11 32417945 2370

===

python Platypus.py callVariants --bamFiles=sample_sort.bam --output=variants.vcf --refFile=hg19.fa --logFileName=log_platypus --nCPU=4 --minFlank=0

188

chr11 32417945 . T C 262 badReads;alleleBias BRF=0.97;FR=0.5000;HP=1;HapScore=1;MGOF=30;MMLQ=38;MQ=60.0;NF=0;NR=24;PP=262;QD=12.3654671895;SC=CAGGCACACGTCGCACATCCT;SbPval=1.0;Source=Platypus;TC=188;TCF=0;TCR=188;TR=24;WE=32417953;WS=32417935 GT:GL:GOF:GQ:NR:NV 1/0:-30.27,0.0,-300.0:30:99:188:24

===

GATK

4998

chr11 32417945 0 T C 11998.81 LowVariantFreq BaseQRankSum=7.009;DP=4998;DS;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=309.8281;MQ=50;MQ0=0;MQRankSum=0.371;QD=2.40;ReadPosRankSum=-1.931;SB=-0.01 GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:4317,669:4998:99:11999,0,159236:50:99:0.134

===

IGV

5671

[Pierre Lindenbaum]

two tools using different filters: min MAPQ, using duplicate, using properly-paired, etc...

[Kevin Blighe]

As per Pierre, this is 'perfectly normal' to see. These tools have different interpretations of what is/is not a high quality read, and will have different default cut-off thresholds. I would save yourself a lot of time by not trying to get them to agree on the read-depth over each position.

Also note that some programs will report high+low quality reads, whilst others will just report high quality ones. Again, what's 'high' and 'low' here is different depending on the program.

Welcome to Bioinformatics.