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anaqib2 started a topic samtools: parse error in SAM to BAM

in Introductions

11-23-2013, 12:58 PM
samtools: parse error in SAM to BAM

Hi

I am trying to convert .sam file to a .bam file using the following script:-

samtools view -bT Ref_HighCov_B07.fa Reads.sam...

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bnfoguy started a topic CIGAR and Sequence length incosistent

in Bioinformatics

06-25-2012, 06:58 AM
CIGAR and Sequence length incosistent

Hello,

I am trying to convert a .sam file into .bam file and I get the following error:

CIGAR and Sequence length are inconsistent....

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efoss started a topic sam to bam conversion error, no @SQ lines in the header, missing header?

in Bioinformatics

09-05-2011, 03:39 PM
sam to bam conversion error, no @SQ lines in the header, missing header?

I have a sam file that I want to convert to a bam file:

samtools view -b -S in.sam > out.bam

I get this error:
...

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