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Old 12-07-2010, 04:04 AM   #1
Mercutio
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Location: Paris

Join Date: Feb 2010
Posts: 8
Default Convert from baf to bam files

Hi everyone,

I'm trying to convert my baf files to bam, because i want to use dindel.

So i use bfast to convert from baf to sam and samtools from sam to bam, but it failed at the bfast step...

If someone knows a better tools or can help me.

here my command line:
Code:
bfast bafconvert -O 4 -f /path_to/hg37all.fa files.baf
The error:
Code:
************************************************************
Reading in reference genome from /path_to/hg37all.fa.nt.brg.
In total read 26 contigs for a total of 3080452622 bases
************************************************************
************************************************************
In function "readInReadGroup": Fatal Error[OpenFileError]. Message: Could not open file for reading.
The file stream error was:: Bad address
 ***** Exiting due to errors *****
************************************************************
I hav the right on all files...

Thanks guys.
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Old 12-07-2010, 05:28 AM   #2
Mercutio
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Location: Paris

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Posts: 8
Default

I try with bfat 0.6.4 e, i got the folowing error:
Quote:
************************************************************
Reading in reference genome from /pathto/bfast_indexes/hs_ref_37.fa.nt.brg.
In total read 64 contigs for a total of 3099369125 bases
************************************************************
Input:s_4_local.baf
Output:s_4_local.sam
Currently on:
0Erreur de segmentation
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Old 12-07-2010, 10:45 AM   #3
newbietonextgen
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Default

the end product of the bfast run is a SAM file (check the manual, page 52). I think you are leaving the "postprocess" part of the program. I then just use samtools to then convert SAM file to a BAM file.

samtools view -bhS bfast.sam bfast.bam
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