Question: I am getting different counts for the number of bases on reference covered by aligned reads.
0
gravatar for Anop Singh Ranawat
15 months ago by
India
Anop Singh Ranawat0 wrote:

samtools mpileup

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

chr11 32417945 T 5671

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samtools depth

samtools depth sample_sort.bam | grep "32417945"

chr11 32417945 2370

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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

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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

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IGV

5671

next-gen • 466 views
ADD COMMENTlink modified 13 months ago by Biostar ♦♦ 20 • written 15 months ago by Anop Singh Ranawat0
1

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

ADD REPLYlink written 15 months ago by Pierre Lindenbaum118k

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 15 months ago by Kevin Blighe39k
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