freebayes parallel

[pziarsolo]

Hi, I am trying to use freebayes parallel but I have found some issues: 1- git clones different files if you clone vcflib or freebayes: [peio]@[udalaitz]:~$ git clone --recursive git://github.com/ekg/vcflib.git [...] [peio]@[udalaitz]:~$ ls vcflib/bin
bed2region vcfclearid vcfindelproximity vcfnobiallelicsnps vcfplotaltdiscrepancy.sh vcfqualfilter vcfremovenonATGC plot_roc.r vcfclearinfo vcfindels vcfnoindels vcfplotsitediscrepancy.r vcfregionreduce vcfsnps vcf2bed.py vcfcomplex vcfmultiallelic vcfnosnps vcfplottstv.sh vcfregionreduce_and_cut vcfsort vcf2sqlite.py vcffirstheader vcfmultiway vcfnulldotslashdot vcfprintaltdiscrepancy.r vcfregionreduce_pipe vcf_strip_extra_headers vcfbiallelic vcfgtcompare.sh vcfmultiwayscripts vcfplotaltdiscrepancy.r vcfprintaltdiscrepancy.sh vcfregionreduce_uncompressed vcfvarstats

[peio]@[udalaitz]:~$ git clone --recursive git://github.com/ekg/freebayes.git [...] [peio]@[udalaitz]:~$ ls freebayes/vcflib/bin
plot_roc.r vcfcomplex vcfmultiway vcfnulldotslashdot vcfprintaltdiscrepancy.r vcfregionreduce_pipe vcfvarstats vcf2sqlite.py vcfgtcompare.sh vcfmultiwayscripts vcfplotaltdiscrepancy.r vcfprintaltdiscrepancy.sh vcfregionreduce_uncompressed vcfbiallelic vcfindelproximity vcfnobiallelicsnps vcfplotaltdiscrepancy.sh vcfqualfilter vcfsnps vcfclearid vcfindels vcfnoindels vcfplotsitediscrepancy.r vcfregionreduce vcfsort vcfclearinfo vcfmultiallelic vcfnosnps vcfplottstv.sh vcfregionreduce_and_cut vcf_strip_extra_headers

vcffirstheader is not in the freebayes standar instalation.

2- After copyng vcffisrheader to the path I am able to run freebayes parallel but it breaks when trying to write the vcffile:

[jope]@[emmy]:~/rafa_celegans/snv_calling$ freebayes-parallel <(fasta_generate_regions.py ../mapping/reference/c_elegans.WS245.fasta.fai 1000000) 104 -f ../mapping/reference/c_elegans.WS245.fasta --min-mapping-quality 30 --min-base-quality 20 --min-alternate-count 3 --min-alternate-fraction 0.2 --mismatch-base-quality-threshold 15 --read-max-mismatch-fraction 0.05 --min-coverage 6 --report-monomorphic --genotype-qualities --report-genotype-likelihood-max ../mapping/bams/*.bam |vcffilter -f "QUAL > 20" |bgzip >celegans_parallel.vcf.gz error: more sample names in header than sample fields samples: AM141 RVM10_5x RVM12_5x RVM12_original RVM1_5x RVM1_original RVM7_6x line: I 1342206 . C . 3.23224e-15 . DP=320;DPB=320;EPPR=3.03744;GTI=0;MQMR=60;NS=7;NUMALT=0;ODDS=0;PAIREDR=0.99375;PQR=0;PRO=0;QR=11149;RO=320;RPPR=6.91895 GT:GQ:DP:RO:QR:AO:QA:GL 0/0:151.283:50:50:1757:.:.:0 0/0:151.283:47:47:1666:.:.:0 0/0:151.283:65:65:2291:.:.:0 0##fileformat=VCFv4.1 Traceback (most recent call last): File "/usr/local/bin/vcffirstheader", line 16, in print line.strip() IOError: [Errno 32] Broken pipe

Any advice to solve this?

Peio

[tseemann]

This is essentially the same problem as #130

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