about problems run into for samtools
Hi,guys,
I created tissue.sam file, using ./bwa samse. I tried to convert the tissue.sam file into tissue.bam, using ./samtools view -bt ref.fa.fai -o tissue.bam tissue.sam
But an error popped up. the error is as follows:
[sam_header_read2] 24 sequences loaded.
Parse error at line 1: invalid CIGAR character
Aborted
Could you kindly help me fix this problem? Thank you a lot.
Btw, I created the ref.fa.fai, using ./samtools faidx ref.fa
The content of the ref.fa.fai is as follows:
gi|224384768|gb|CM000663.1| 249250621 87 70 71
gi|224384767|gb|CM000664.1| 243199373 252811519 70 71
gi|224384766|gb|CM000665.1| 198022430 499485256 70 71
gi|224384765|gb|CM000666.1| 191154276 700336665 70 71
gi|224384764|gb|CM000667.1| 180915260 894221804 70 71
gi|224384763|gb|CM000668.1| 171115067 1077721655 70 71
gi|224384762|gb|CM000669.1| 159138663 1251281310 70 71
gi|224384761|gb|CM000670.1| 146364022 1412693470 70 71
gi|224384760|gb|CM000671.1| 141213431 1561148494 70 71
gi|224384759|gb|CM000672.1| 135534747 1704379348 70 71
gi|224384758|gb|CM000673.1| 135006516 1841850394 70 71
gi|224384757|gb|CM000674.1| 133851895 1978785663 70 71
gi|224384756|gb|CM000675.1| 115169878 2114549816 70 71
gi|224384755|gb|CM000676.1| 107349540 2231365066 70 71
gi|224384754|gb|CM000677.1| 102531392 2340248259 70 71
gi|224384753|gb|CM000678.1| 90354753 2444244474 70 71
gi|224384752|gb|CM000679.1| 81195210 2535890098 70 71
gi|224384751|gb|CM000680.1| 78077248 2618245328 70 71
gi|224384750|gb|CM000681.1| 59128983 2697438054 70 71
gi|224384749|gb|CM000682.1| 63025520 2757411825 70 71
gi|224384748|gb|CM000683.1| 48129895 2821337798 70 71
gi|224384747|gb|CM000684.1| 51304566 2870155351 70 71
gi|224384746|gb|CM000685.1| 155270560 2922192927 70 71
gi|224384745|gb|CM000686.1| 59373566 3079681725 70 71
I created tissue.sam file, using ./bwa samse. I tried to convert the tissue.sam file into tissue.bam, using ./samtools view -bt ref.fa.fai -o tissue.bam tissue.sam
But an error popped up. the error is as follows:
[sam_header_read2] 24 sequences loaded.
Parse error at line 1: invalid CIGAR character
Aborted
Could you kindly help me fix this problem? Thank you a lot.
Btw, I created the ref.fa.fai, using ./samtools faidx ref.fa
The content of the ref.fa.fai is as follows:
gi|224384768|gb|CM000663.1| 249250621 87 70 71
gi|224384767|gb|CM000664.1| 243199373 252811519 70 71
gi|224384766|gb|CM000665.1| 198022430 499485256 70 71
gi|224384765|gb|CM000666.1| 191154276 700336665 70 71
gi|224384764|gb|CM000667.1| 180915260 894221804 70 71
gi|224384763|gb|CM000668.1| 171115067 1077721655 70 71
gi|224384762|gb|CM000669.1| 159138663 1251281310 70 71
gi|224384761|gb|CM000670.1| 146364022 1412693470 70 71
gi|224384760|gb|CM000671.1| 141213431 1561148494 70 71
gi|224384759|gb|CM000672.1| 135534747 1704379348 70 71
gi|224384758|gb|CM000673.1| 135006516 1841850394 70 71
gi|224384757|gb|CM000674.1| 133851895 1978785663 70 71
gi|224384756|gb|CM000675.1| 115169878 2114549816 70 71
gi|224384755|gb|CM000676.1| 107349540 2231365066 70 71
gi|224384754|gb|CM000677.1| 102531392 2340248259 70 71
gi|224384753|gb|CM000678.1| 90354753 2444244474 70 71
gi|224384752|gb|CM000679.1| 81195210 2535890098 70 71
gi|224384751|gb|CM000680.1| 78077248 2618245328 70 71
gi|224384750|gb|CM000681.1| 59128983 2697438054 70 71
gi|224384749|gb|CM000682.1| 63025520 2757411825 70 71
gi|224384748|gb|CM000683.1| 48129895 2821337798 70 71
gi|224384747|gb|CM000684.1| 51304566 2870155351 70 71
gi|224384746|gb|CM000685.1| 155270560 2922192927 70 71
gi|224384745|gb|CM000686.1| 59373566 3079681725 70 71
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