Tweet
Hello all,
I have a SAM file create with BWA, but I cannot convert it to BAM because of the following:
samtools view -S foo.sam -b -o foo.bam
[samopen] no @SQ lines in the header.
[main_samview] random alignment retrieval only works for indexed BAM files.
The SAM file looks like this:
head foo.sam
5_gECOjxwXsN1 0 contig00025 28520 37 35M = 28520 0 AACGNTACTATCGTGACATGCGTGCAGGATTACAC abb^D[a`ab^`Y`a_[___^[ON\X`_Y]`_aa\ XT:A:U NM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:4T30
3_8ICOjxwXsN1 4 * 0 0 * * 0 0 ACTCNAGGGTTCGATTCCCTTCAACCGCCCCATAA a`WYD[aaaW_^_[^^W`]`]\^`\V][[_]QV\\
3_GUCOjxwXsN1 4 * 0 0 * * 0 0 TTGCNTCCTTCTTCTGCCTTCGTTGGCTCAGATTG `aaYDRb_a[a`]^X^`]`aa`]XVT]R[^`TZVY
5_BWCOjxwXsN1 0 contig00138 59297 37 35M = 59297 0 TATATACAGGAATCCATTGTTGTTTAGATTCAGTT ab`b`baaaa`b``ZY]YW^aS[_]OLT_VRS]UZ XT:A:U NM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:35
7_NZCOjxwXsN1 16 contig00115 1617 37 35M = 1617 0 AGGTAGCCGTATCGGAAGGTGCGGCTGGATCACCT MSKNT\V^TSWW`\`Z^Z\Q\\___a`a_`ZDY`] XT:A:U NM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:35
3_2VCOjxwXsN1 16 contig00005 66001 37 35M = 66001 0 CTTAATGGGTGAAGATGTCTACACACCTGGAAAAG aaaaa`a``aa_aaaa`aab_b`b[aabaaaabaa XT:A:U NM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:35
5_kVCOjxwXsN1 4 * 0 0 * * 0 0 CTACACCTAAGTTACATCGTCCATTATTTTCCAAT aaaaaaaabaa_aa_a__a^a[[``\a`a][\`[_
1_GbCOjxwXsN1 0 contig00105 1098 37 35M = 1098 0 CCAGACAACTAGGATGTTGGCTTAGAAGCAGCCAT ```_aabaaa`ba`Y`S[_`_^]a^a`_YaYSUXT XT:A:U NM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:35
5_fTCOjxwXsN1 4 * 0 0 * * 0 0 TTAGCTTTAACCATTTTCTTTTTGTCTAAAGCAAA aabb__\_aaabU_^^[^`[\_`aWaa``_^a``_
3_VWCOjxwXsN1 16 contig00027 14175 37 35M = 14175 0 GTTTAACGCGTTCACGTTCGCCACGCGCATCATAA T\`a\\a]]V]aa_aaaaaaaaY`abab_aaabba XT:A:U NM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:35
Suggestions are welcome.
Martin
I have a SAM file create with BWA, but I cannot convert it to BAM because of the following:
samtools view -S foo.sam -b -o foo.bam
[samopen] no @SQ lines in the header.
[main_samview] random alignment retrieval only works for indexed BAM files.
The SAM file looks like this:
head foo.sam
5_gECOjxwXsN1 0 contig00025 28520 37 35M = 28520 0 AACGNTACTATCGTGACATGCGTGCAGGATTACAC abb^D[a`ab^`Y`a_[___^[ON\X`_Y]`_aa\ XT:A:U NM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:4T30
3_8ICOjxwXsN1 4 * 0 0 * * 0 0 ACTCNAGGGTTCGATTCCCTTCAACCGCCCCATAA a`WYD[aaaW_^_[^^W`]`]\^`\V][[_]QV\\
3_GUCOjxwXsN1 4 * 0 0 * * 0 0 TTGCNTCCTTCTTCTGCCTTCGTTGGCTCAGATTG `aaYDRb_a[a`]^X^`]`aa`]XVT]R[^`TZVY
5_BWCOjxwXsN1 0 contig00138 59297 37 35M = 59297 0 TATATACAGGAATCCATTGTTGTTTAGATTCAGTT ab`b`baaaa`b``ZY]YW^aS[_]OLT_VRS]UZ XT:A:U NM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:35
7_NZCOjxwXsN1 16 contig00115 1617 37 35M = 1617 0 AGGTAGCCGTATCGGAAGGTGCGGCTGGATCACCT MSKNT\V^TSWW`\`Z^Z\Q\\___a`a_`ZDY`] XT:A:U NM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:35
3_2VCOjxwXsN1 16 contig00005 66001 37 35M = 66001 0 CTTAATGGGTGAAGATGTCTACACACCTGGAAAAG aaaaa`a``aa_aaaa`aab_b`b[aabaaaabaa XT:A:U NM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:35
5_kVCOjxwXsN1 4 * 0 0 * * 0 0 CTACACCTAAGTTACATCGTCCATTATTTTCCAAT aaaaaaaabaa_aa_a__a^a[[``\a`a][\`[_
1_GbCOjxwXsN1 0 contig00105 1098 37 35M = 1098 0 CCAGACAACTAGGATGTTGGCTTAGAAGCAGCCAT ```_aabaaa`ba`Y`S[_`_^]a^a`_YaYSUXT XT:A:U NM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:35
5_fTCOjxwXsN1 4 * 0 0 * * 0 0 TTAGCTTTAACCATTTTCTTTTTGTCTAAAGCAAA aabb__\_aaabU_^^[^`[\_`aWaa``_^a``_
3_VWCOjxwXsN1 16 contig00027 14175 37 35M = 14175 0 GTTTAACGCGTTCACGTTCGCCACGCGCATCATAA T\`a\\a]]V]aa_aaaaaaaaY`abab_aaabba XT:A:U NM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:35
Suggestions are welcome.
Martin
).
Comment