Hi all,
I had problems in using SAMtools to call the variations from a BFAST- aligned SAM file.
The commands I used:
$ samtools-0.1.7/samtools view -bS -q 20 bfast.aln.sam > bfast.aln.bam
$ samtools-0.1.7/samtools sort bfast.aln.bam bfast-aln.sorted
$ samtools-0.1.7/samtools index bfast-aln.sorted.bam
$ samtools-0.1.7/samtools pileup -vcf TAIR9genomeSeq.txt bfast-aln.sorted.bam | tee bfast-raw.txt | samtools-0.1.7/samtools.pl varFilter -D100 > bfast-flt.txt
It had run for days in pileup step, with no error information and no output.
The SAMtools worked fine with the BWA-aligned sam file from the same data.
Is anything wrong with my Bfast-sam file? which look like:
@HD VN:0.1.2
@SQ SN:Chr1 LN:30427671
@SQ SN:Chr2 LN:19698289
@SQ SN:Chr3 LN:23459830
@SQ SN:Chr4 LN:18585056
@SQ SN:Chr5 LN:26975502
@SQ SN:chloroplast LN:154478
@SQ SN:mitochondria LN:366924
@PG ID:bfast VN:0.6.2a
HWI-EAS412:2:1:0:1469#0/1 4 * 0 0 * * nttcctatcaaggttaaggagtcaactgagcatctcagcggcgggattgaatacccggatcgaatcagagttcacg DOXVYWYWWWWVWWYYWWTWVWWWWWWWWYWYWWYWUSVYVWWWVNUUSUWWWQUGVRRRUPTUPWUUWTVSLRPU PG:Z:bfast AS:i:-2147483648 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:* XA:i:3
HWI-EAS412:2:1:1:1078#0/1 4 * 0 0 * * ncgccccggccgatatcctcaaccagctggccacgtagatcggaagagctcgtatgccgtcttcttctttaaaaaa DNVUWXXVWWSUVWWXUUWWVWWUWWVNSUURWQVWUSXWUUUUWWSSNUNSVWWFNJNVVVVQTKOVSGOVSUVS PG:Z:bfast AS:i:-2147483648 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:* XA:i:3
HWI-EAS412:2:1:1:660#0/1 16 Chr3 13591936 10 76M tgattaagtataagaacttaaaccgcaacatgatcttaaaggcgtaagaattgtatccttgttaaaagacacaaan BBXXXZ[[Z[Y[WWW[[[[[YVRVY[[[[YZY[ZYULV[[ZYY[[[ZZZ[[[[[[XVSX[[[[[[[[ZYYYVY[OD PG:Z:bfast AS:i:3000 NM:i:4 NH:i:1 IH:i:1 HI:i:1 MD:Z:5G23CC44G XA:i:3
HWI-EAS412:2:1:1:1493#0/1 0 Chr1 14102811 40 76M natcttcttgaagtgtgaaatacttcatcaaacggtggagaatacttctcccttggtcactcgatcaaacggtgag DOZZZZZZYYYYYXSXYYZZZZXZZZZZXZZZZXZZYYYXZZZZZZZZZYVXZZYWYWZZZXZZXXZZZZUURZXV PG:Z:bfast AS:i:3600 NM:i:1 NH:i:1 IH:i:1 HI:i:1 MD:Z:T75 XA:i:3
HWI-EAS412:2:1:1:1133#0/1 16 Chr4 3403799 50 76M * gtttgttctctcacttggcgagcaatacggtcgatgttatcgttgaatagaaggttctgaattccttgtgaccgtn BTWYYWYVYWWWTVWVYYWWYSSVYYVSTVWYWZZZXZZYWYZXZZZZZZZYYYZWSWYYZZWUUWZZYYVPLTOD PG:Z:bfast AS:i:3600 NM:i:1 NH:i:1 IH:i:1 HI:i:1 MD:Z:75G XA:i:3
HWI-EAS412:2:1:1:144#0/1 16 Chr2 15897161 255 76M agtaccgaatcgttggatgatgatggtagtgatgatcgtggtggtaatgagatccgctagaggaggaaccatttgn YYXWUWVWYWVWYVVUVYUYXWYXYXYYYYYYYYYXYYYYXYYYXYYYYYYYYYYYXYYXYYYYYYYYYYURUYOD PG:Z:bfast AS:i:3400 NM:i:2 NH:i:1 IH:i:1 HI:i:1 MD:Z:71A3A XA:i:3
HWI-EAS412:2:1:1:502#0/1 4 * 0 0 * * ntcttagatctcacaaaaaagaccaaaagtaattcaactgatgaatttagataaagtaatttgtcttctaaaccca DP[[[ZYZ[[[[[[[[[[[ZYZ[[YYYYXY[[[[[Z[[[[[[[[Z[[[YTYZ[[[[Y[Z[[XXXY[[W[YYXURVW PG:Z:bfast AS:i:-2147483648 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:* XA:i:3
HWI-EAS412:2:1:1:1922#0/1 0 mitochondria 210296 255 76M naagagcaaagcgtggctttttgccccggggcactagggcctgatcatctttatggctataaatctggcttccaag DOWWXWXYWYYYYWYYWYYYYWTUWXWXWWWWWWWWWXWWVWWYWWWWWWYWWWBBBBBBBBBBBBBBBBBBBBBB PG:Z:bfast AS:i:3000 NM:i:4 NH:i:1 IH:i:1 HI:i:1 MD:Z:C66C4AC2 XA:i:3
HWI-EAS412:2:1:1:1659#0/1 16 Chr2 18335755 255 76M ggcaggaacaaacagaaacagacagagtcgaaaacaaattcgtcgaatgataatagtagtaaacaagacacaggtn BTOTQOSYVYYXYXXXYYYXXXZZZZZZZXZZZZZZZZZZZZYXYZZZZZZZZZZZZZZXZZYYYZZZXZZZZZND PG:Z:bfast AS:i:3600 NM:i:1 NH:i:1 IH:i:1 HI:i:1 MD:Z:75A XA:i:3
HWI-EAS412:2:1:1:477#0/1 0 Chr3 18560494 255 76M natgtggttcagttttgtatggtttttttgtctgtgactatttgttaatggtacgtttttgaatgccccaaatcaa DM[[WSSLPWY[W[Y[[WZ[W[ZYVYYYY[[VZYSVYXZX[XXTYYVYXPXVSRT[YYYXXRUXXSYLQQUXXSUX PG:Z:bfast AS:i:3600 NM:i:1 NH:i:1 IH:i:1 HI:i:1 MD:Z:A75 XA:i:3
HWI-EAS412:2:1:1:1430#0/1 0 Chr4 4184778 28 76M * ntcgagtagtttcgtttcctcagtttacaagtgattgacatgctcaataaattaccctacacaacaagttcattaa DOVUXXXVXXXTTRVXYVTVYXXXZZZVTSYXXXYYYTTTXVVVXTXXYVXXYYVRTVVUWWSSOQVTXSOQYYTT PG:Z:bfast AS:i:3600 NM:i:1 NH:i:1 IH:i:1 HI:i:1 MD:Z:A75 XA:i:3
My reads are 76 bp and I used bfast-0.6.2a
Thank you very much for your attention and help!
Ling
I had problems in using SAMtools to call the variations from a BFAST- aligned SAM file.
The commands I used:
$ samtools-0.1.7/samtools view -bS -q 20 bfast.aln.sam > bfast.aln.bam
$ samtools-0.1.7/samtools sort bfast.aln.bam bfast-aln.sorted
$ samtools-0.1.7/samtools index bfast-aln.sorted.bam
$ samtools-0.1.7/samtools pileup -vcf TAIR9genomeSeq.txt bfast-aln.sorted.bam | tee bfast-raw.txt | samtools-0.1.7/samtools.pl varFilter -D100 > bfast-flt.txt
It had run for days in pileup step, with no error information and no output.
The SAMtools worked fine with the BWA-aligned sam file from the same data.
Is anything wrong with my Bfast-sam file? which look like:
@HD VN:0.1.2
@SQ SN:Chr1 LN:30427671
@SQ SN:Chr2 LN:19698289
@SQ SN:Chr3 LN:23459830
@SQ SN:Chr4 LN:18585056
@SQ SN:Chr5 LN:26975502
@SQ SN:chloroplast LN:154478
@SQ SN:mitochondria LN:366924
@PG ID:bfast VN:0.6.2a
HWI-EAS412:2:1:0:1469#0/1 4 * 0 0 * * nttcctatcaaggttaaggagtcaactgagcatctcagcggcgggattgaatacccggatcgaatcagagttcacg DOXVYWYWWWWVWWYYWWTWVWWWWWWWWYWYWWYWUSVYVWWWVNUUSUWWWQUGVRRRUPTUPWUUWTVSLRPU PG:Z:bfast AS:i:-2147483648 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:* XA:i:3
HWI-EAS412:2:1:1:1078#0/1 4 * 0 0 * * ncgccccggccgatatcctcaaccagctggccacgtagatcggaagagctcgtatgccgtcttcttctttaaaaaa DNVUWXXVWWSUVWWXUUWWVWWUWWVNSUURWQVWUSXWUUUUWWSSNUNSVWWFNJNVVVVQTKOVSGOVSUVS PG:Z:bfast AS:i:-2147483648 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:* XA:i:3
HWI-EAS412:2:1:1:660#0/1 16 Chr3 13591936 10 76M tgattaagtataagaacttaaaccgcaacatgatcttaaaggcgtaagaattgtatccttgttaaaagacacaaan BBXXXZ[[Z[Y[WWW[[[[[YVRVY[[[[YZY[ZYULV[[ZYY[[[ZZZ[[[[[[XVSX[[[[[[[[ZYYYVY[OD PG:Z:bfast AS:i:3000 NM:i:4 NH:i:1 IH:i:1 HI:i:1 MD:Z:5G23CC44G XA:i:3
HWI-EAS412:2:1:1:1493#0/1 0 Chr1 14102811 40 76M natcttcttgaagtgtgaaatacttcatcaaacggtggagaatacttctcccttggtcactcgatcaaacggtgag DOZZZZZZYYYYYXSXYYZZZZXZZZZZXZZZZXZZYYYXZZZZZZZZZYVXZZYWYWZZZXZZXXZZZZUURZXV PG:Z:bfast AS:i:3600 NM:i:1 NH:i:1 IH:i:1 HI:i:1 MD:Z:T75 XA:i:3
HWI-EAS412:2:1:1:1133#0/1 16 Chr4 3403799 50 76M * gtttgttctctcacttggcgagcaatacggtcgatgttatcgttgaatagaaggttctgaattccttgtgaccgtn BTWYYWYVYWWWTVWVYYWWYSSVYYVSTVWYWZZZXZZYWYZXZZZZZZZYYYZWSWYYZZWUUWZZYYVPLTOD PG:Z:bfast AS:i:3600 NM:i:1 NH:i:1 IH:i:1 HI:i:1 MD:Z:75G XA:i:3
HWI-EAS412:2:1:1:144#0/1 16 Chr2 15897161 255 76M agtaccgaatcgttggatgatgatggtagtgatgatcgtggtggtaatgagatccgctagaggaggaaccatttgn YYXWUWVWYWVWYVVUVYUYXWYXYXYYYYYYYYYXYYYYXYYYXYYYYYYYYYYYXYYXYYYYYYYYYYURUYOD PG:Z:bfast AS:i:3400 NM:i:2 NH:i:1 IH:i:1 HI:i:1 MD:Z:71A3A XA:i:3
HWI-EAS412:2:1:1:502#0/1 4 * 0 0 * * ntcttagatctcacaaaaaagaccaaaagtaattcaactgatgaatttagataaagtaatttgtcttctaaaccca DP[[[ZYZ[[[[[[[[[[[ZYZ[[YYYYXY[[[[[Z[[[[[[[[Z[[[YTYZ[[[[Y[Z[[XXXY[[W[YYXURVW PG:Z:bfast AS:i:-2147483648 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:* XA:i:3
HWI-EAS412:2:1:1:1922#0/1 0 mitochondria 210296 255 76M naagagcaaagcgtggctttttgccccggggcactagggcctgatcatctttatggctataaatctggcttccaag DOWWXWXYWYYYYWYYWYYYYWTUWXWXWWWWWWWWWXWWVWWYWWWWWWYWWWBBBBBBBBBBBBBBBBBBBBBB PG:Z:bfast AS:i:3000 NM:i:4 NH:i:1 IH:i:1 HI:i:1 MD:Z:C66C4AC2 XA:i:3
HWI-EAS412:2:1:1:1659#0/1 16 Chr2 18335755 255 76M ggcaggaacaaacagaaacagacagagtcgaaaacaaattcgtcgaatgataatagtagtaaacaagacacaggtn BTOTQOSYVYYXYXXXYYYXXXZZZZZZZXZZZZZZZZZZZZYXYZZZZZZZZZZZZZZXZZYYYZZZXZZZZZND PG:Z:bfast AS:i:3600 NM:i:1 NH:i:1 IH:i:1 HI:i:1 MD:Z:75A XA:i:3
HWI-EAS412:2:1:1:477#0/1 0 Chr3 18560494 255 76M natgtggttcagttttgtatggtttttttgtctgtgactatttgttaatggtacgtttttgaatgccccaaatcaa DM[[WSSLPWY[W[Y[[WZ[W[ZYVYYYY[[VZYSVYXZX[XXTYYVYXPXVSRT[YYYXXRUXXSYLQQUXXSUX PG:Z:bfast AS:i:3600 NM:i:1 NH:i:1 IH:i:1 HI:i:1 MD:Z:A75 XA:i:3
HWI-EAS412:2:1:1:1430#0/1 0 Chr4 4184778 28 76M * ntcgagtagtttcgtttcctcagtttacaagtgattgacatgctcaataaattaccctacacaacaagttcattaa DOVUXXXVXXXTTRVXYVTVYXXXZZZVTSYXXXYYYTTTXVVVXTXXYVXXYYVRTVVUWWSSOQVTXSOQYYTT PG:Z:bfast AS:i:3600 NM:i:1 NH:i:1 IH:i:1 HI:i:1 MD:Z:A75 XA:i:3
My reads are 76 bp and I used bfast-0.6.2a
Thank you very much for your attention and help!
Ling
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