Mapping Illumina data with smalt

[adippenaar]

I have paired end Illumina data and currently I am using different algorithms to map and call SNPs in order to make high confidence variant calls.

When using smalt to map (version 0.6.2), the resulting sam file gives the following error in the sam validation file when validating with Picard:

WARNING: Record 1, Read name HWUSI-EAS1501:32:FC638CYAAXX:1:1:1470:953, NM tag (nucleotide differences) is missing

I have tried to add read groups with Picard, also without any success. Error as follows:

Exception in thread "main" net.sf.samtools.SAMFormatException: Error parsing text SAM file. Zero-length read without CS or CQ tag; File 2262_trim35_smalt_noHD.sam; Line 42
Line: HWUSI-EAS1501:32:FC638CYAAXX:1:1:17213:965 69 * 0 0 * H37Rv 4055892 0 * * AS:i:0


Any input on how to manipulate the sam file from smalt in order for it to be Picard and GATK friendly would be greatly appreciated. I have used novoalign and bwa and the downstream Picard and GATK analyses run smoothly. Could you please advise?

[kksiame]

We managed to present the same problem outlined by adippenaar to the the author of SMALT (Hannes Ponstingl). Here is the suggestion they gave:

> samtools calmd -bS <smalt_sam_output_file> <fasta_reference_seqences> > <bam_with_NM>
then view the NM tag:
> samtools view <bam_with_NM>