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I've been using the SMRT analysis suite and recently ran into an issue. the reads of insert mapping and resequencing protocols are not spitting out .bam files for a couple of reference genomes that i'm using (some of the reference builds are fine however). the .sam file that's being generated during the mapping contains "Z" CIGAR operators and samtools throws the error invalid operator error during conversion, hence no .bam file. Do the Z CIGAR operators mean anything or is this a software bug of some sort?
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Can you provide a couple of lines of the SAM files with the Z in the CIGAR string? -
yeah sure. I have a workaround at the moment so it's not urgent or anything. I ran an independent install of blasr of the reads of insert against the same reference and output a sam file, no Z operations, so I think it's either blasr outputting a h5 or pbsamtools converting h5->sam.
...2M1Z14M1I1M1D22M1D10M1I28M1I4M1D9M1I6M1I12M1I10M1I36M1I2M1D6M2I7M1I1M1D17M1D9M1I
20M1D3M1I2M1I14M1I2M1I6M2D45M1I24M1I8M1D3M1I7M1I42M2I8M1I7M1D22M3I3M1I5M1I1M1I12M1I4M1I32M1I3M
1I9M1I10M1I3M1I9M1I1M1I2M1D4M1I2M1I2M1I8M1I49M1I16M1I7M1I1M1D8M1D3M1I1M1I10M1I1M1I8M1I12M1D4M1I
13M1I6M1D23M1I11M1D21M2D4M1I6M1I28M1I6M1I4M1D17M1D1M1I7M1I13M1I12M1I18M1I3M1I8M1D4M1I5M2I9M1I
9M1I7M1I19M1I22M1I19M1I6M1I11M1I14M1D9M1D12M2D14M1I5M1D5M1I1M1I6M3I25M2I14M1I6M1I9M1D9M1I1M1D
5M1I2M1I9M1D2M1D5M1I12M1I34M1I14M1I21M1D9M1I3M1I4M1I9M1D4M1I8M1I19M1I8M1I19M1I3M1I1M1I25M1I5M1I
7M1I39M1I8M1I44M1D4M1I8M1I11M1D2M1I21M1D2M2I5M1D1M1D3M1D10M1D2M1D5M1I21M1I40M1I7M1I4M1D12M
1D9M2I8M1I30M1D5M1D4M2I2M1D7M1D16M1I7M1I2M1I11M1I2M1I14M1D2M1I3M1I21M1I2M1D9M1I39M1D4M1D21M1I
5M1I12M1D6M1I25M1D1M1D3M1D2M1I1M1I25M1I4M1D33M1I9M1I9M1D3M1D6M1D5M1I30M1I3M1I12M1D3M1I10M1I8M
1I29M1I1M1I4M1D10M1I2M1I13M1I7M1Z31M...Last edited by BeardyMcJohnFace; 04-14-2016, 03:46 PM.Comment
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