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Old 01-22-2013, 10:10 AM   #21
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Location: Worcester, MA

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Using pileup with the -f argument allows you to supply the faidx indexed reference sequence file. I used this option and it fixed my problem.
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Old 03-05-2013, 12:49 PM   #22
Location: New Jersey

Join Date: Aug 2010
Posts: 29
Default Same problem

Did you find a solution to the null problem please?

Originally Posted by ericpante View Post
Hi everybody,

I am have similar problems with samtools 0.1.18. I would like to have reference characters listed in a pileup files, but I have problems with headers.

samtools faidx AGSbrut.fasta
samtools view -q 20 -buh -t AGSbrut.fasta.fai A.sam | samtools sort - A
samtools view -q 20 -buh -t AGSbrut.fasta.fai S.sam | samtools sort - S
samtools mpileup -B -f AGSbrut_index.fai A.bam S.bam > AS.mpileup

[fai_build_core] different line length in sequence 'null'.
Segmentation fault

I hypothesized that this 'null' sequence may be a blank line; so I looked for it manually and with sed, with no luck. I also looked for other potential problems based on what was previously reported (no extra spaces, characters, etc in reference sequence names in fai and sam files). I also tried to re-head the file, with no success:

samtools view -HS -t AGSbrut.fasta.fai A.sam > Aheader.sam
samtools reheader Aheader.sam A.bam > Aheaded.bam

[bam_header_read] EOF marker is absent. The input is probably truncated.

All insights are welcome!
thank you, eric
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mosaik, pileup, reference, samtools

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