Question: I am getting different counts for the number of bases on reference covered by aligned reads.
gravatar for Anop Singh Ranawat
21 months ago by
Anop Singh Ranawat0 wrote:

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


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




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




next-gen • 568 views
ADD COMMENTlink modified 19 months ago by Biostar ♦♦ 20 • written 21 months ago by Anop Singh Ranawat0

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

ADD REPLYlink written 21 months ago by Pierre Lindenbaum122k

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.

ADD REPLYlink written 21 months ago by Kevin Blighe46k
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