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Variant calling with paired-end reads fails #5
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I'm travelling at the moment - will look at fixing For the second issue, the
Hope that helps. Thank you for trying cortex. Isaac |
Hi Thanks for the answer. I tried the first command
but it produced another error:
Is it comparing the names of different samples in the same file? |
I'm trying to resolve this issue at the moment. For now you should be able to work around it by only loading one sample at a time. This is not ideal, but I'll put up a fix shortly.
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Fixes issue #5 1. Only use seed kmers that are in the sample we are pulling out contigs for 2. Allow pooling colours when checking sample names match 3. graph_file_reader.c, gpath_reader.c: paths are const char* not char* now 4. db_alignment.c: keep track of kmer origin position or -1 if inferred kmer 5. correct_alignment.c: operates on internal dBAlignment and takes reads as input 6. Print VCF header from JSON input headers 7. gpath_load_sample_pop() now won't complain if you give multi-colour graph file and only ask to load a single colour from it. 8. assemble_contigs.c: When pulling out a contig, give end status as HitRepeat if GraphWalker ok but RepeatWalker stopped.
Hello
I tried to follow the "Workflow Examples" in the wiki to do variant calling with two plant genotypes based on paired end reads. Here is the sequence of commands I used:
Unfortunately, both read threading steps failed with this error:
I tried to "fix" this by adding this code above line 135 in alignment/correct_aln_stats.c:
After recompiling the threading runs smooth. However, now I am stuck at the contigs command
which yields:
Any clues what went wrong?
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