SAM-to-BAM Error

[icymiktreize]

Hello everyone,
I have this problem when using Picard to convert my SAM files to BAM files (I used BWA-MEM for mapping my reads)
Exception in thread "main" htsjdk.samtools.SAMFormatException: Error parsing tex t SAM file. Empty field at position 9 (zero-based); File BC002.sam; Line 31944
Line: 04JBV:00098:00810 4 * 0 0 * * 0 0 * AS:i:0 XS:i:0

Anyone can help me to solve this problems? Many thanks.

[dpryan]

The error message is actually wrong in this case, which would appear to be a bug. The problem is that there are only 10 non-auxiliary fields in that line, so the QUAL field is completely missing. A valid version of that line should be:

04JBV:00098:00810       4       *       0       0       *       *       0       0       *       *       AS:i:0  XS:i:0

[icymiktreize]

The error message is actually wrong in this case, which would appear to be a bug. The problem is that there are only 10 non-auxiliary fields in that line, so the QUAL field is completely missing. A valid version of that line should be:

04JBV:00098:00810       4       *       0       0       *       *       0       0       *       *       AS:i:0  XS:i:0

Thanks for your answer. Do you know what I can do to fix this bug?

[dpryan]

The simplest solution would be to just ignore that line:

 awk '{if(NR != 31944) print $0}' foo.sam | samtools view -Sbo foo.bam -

You could substitute picard for samtools, in which case you'd need to use "I=/dev/stdin" in place of "-".