gaps in consensus obtained from align (BAM) files though genome browser shows coverage?

Hi, I am a newbie to NGS data.

I was trying to extract consensus from BAM files of 1000genomedata (namely ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/data/NA12878/alignment/NA12878.chrom8.SOLID.bfast.CEU.high_coverage.20100125.bam 8:125807080-126007080) by samtools pileup consensus calling (ref: hg19 human_g1k_v37.fasta.gz )

I found some bases/positions like bases between position 125906527 and 125906541.

What might be the reason? Can you guys please help me to obtains those missing bases?

Thanks a lot, Culmen

samtools data extraction consensus

asked 21 Jul '10, 13:24

culmen
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Asked: 21 Jul '10, 13:24

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Last updated: 22 Jul '10, 01:09

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